Legal framework on freedom of religion and actual application
The Peace Agreement signed in August 2015 by South Sudan President Salva Kiir and rebel groups  stipulated that, 18 months after the establishment of the Transitional Government of National Unity, there would be a new constitution accommodating points included in the earlier agreement. A draft constitution, known as the Transitional Constitution Amendment Bill, was approved by the government in November 2017. At the time of writing, no amendments from the Peace Agreements had been incorporated into the constitution.
The current transitional constitution, ratified on Independence Day (9th July 2011) and subsequently amended in 2013 and 2015, enshrines in article 8 the separation between religion and state, and guarantees all religious groups are treated equally. Article 23 details religious rights in the country.
In general, there is a high degree of tolerance in society towards religious groups. Christian and Muslim groups share common initiatives. Religious groups are able to register with the Ministry of Human Affairs through the Relief and Rehabilitation Commission.
Recently the National Communication Authority has implemented an annual payment of US$ 5,500 from each of the nine radio stations affiliated to the Catholic Radio Network. It is not known whether such charges apply to other faith-based stations but, in any case, this very costly fee threatens the economic viability of existing Catholic stations.
The security situation in different parts of the country has very much deteriorated during the current reporting period. Despite truces and peace agreements, lasting and meaningful peace is very far from reality for most South Sudanese, with several basic liberties at risk on a daily basis. Furthermore, political leaders and government officials, are often accused of failing to protect the civilian population.
South Sudan’s present security situation over the last few years, apart from being very serious, has huge implications as regards freedom of speech for faith-based groups. In recent years, numerous massacres and atrocities have taken place in the country, with the perpetrators often enjoying total impunity. Between 50,000 and 300,000 people have died in armed conflict over the last four years. 
Faith-based groups and organisations are at the forefront of the aid offered to displaced persons and to victims and casualties of the armed conflict. Churches and other places of worship often serve as sanctuaries for thousands of people who have fled their homes.
The prevailing insecurity, the deteriorating rule of law and the wide availability of small weapons enable armed robbers and criminals to target parish houses, church vehicles, convents, religious agencies and presbyteries. According to research carried out by a local radio station, around 40 religious leaders were killed between 2013 and 2017.
Given the lack of ethics within the government and among the political elite in South Sudan, where security forces are suspected of being responsible for two-thirds of human rights violations, religious leaders are often the only social actors with credible moral authority, able to challenge those in power and denounce acts of violence and injustice. This prophetic role often jeopardises the personal safety of those faith leaders who speak out. Some religious leaders have shunned the celebration of the National Day of Prayer called by the President, accusing him of being one of the root causes of the present armed conflict.
Radio Bakhita, a Juba-based Catholic radio station, was harassed several times by security officers after it broadcast the homily of a high-ranking Catholic priest who heavily criticised the government and the opposition.
A priest belonging to the Mundri Diocese of the Episcopal Church of Sudan was arrested, tortured and executed, allegedly on orders of the state governor, after he was accused of providing food to units of a rebel movement known as Sudan People’s Liberation Movement In Opposition (SPLM-IO).
Local authorities in Gbudue state closed down a church called Gundeti Mbori Catholic Church, Genezareth on charges of operating irregularly and of false affiliation to the Roman Catholic Church. Local church leaders were allegedly asking HIV-patients among the congregation to stop taking their medication.
A lay catechist in charge of the Mondikolok chapel in the Catholic Parish of Lomin (Kajo-Keji County) was killed together with four other people during clashes between government and opposition forces. According to church sources, he worked for dialogue and reconciliation between warring parties.
Three clergy from the Episcopal Church of Sudan were killed in early 2017. Rev Simon Kwaje, a priest working at the Emmanuel Cathedral, was found dead in Yei town on 12th March 2017. The motives behind the murder and the identity of the assailants were unknown. Rev Wilson Tatawa was killed on 26th March 2017 at Kundi village, in Mundari East County/Amadi State. Rev Mathew Mangok Alek was shot dead by unknown gunmen on 18th April 2017 in Gargar village, Tonj state, while he was travelling along the Tonj-Mapel road.
Joel Mwendwa, an Evangelical bishop of Kenyan origin, was killed with a machete in the Juba suburb of Munuki in the early hours of 24th June 2017. The assailant was arrested by police and he accused the clergyman of constantly disturbing him with noisy activities taking place at the church.
The female coordinator of the Peace and Justice Department of the Catholic Diocese of Wau was arrested after taking part in a UN-organised workshop on human rights for the military, where three participating army officers died of food poisoning. The precise charges laid against her were unclear.
On 5th February 2018, a Kenyan Catholic priest from the Diocese of Tombura-Yambio was expelled by authorities of Tombura state following an order issued by Minister Joseph Marko Wanga Bilali. The missionary was taken by plane to Kenya. A subsequent statement by the local bishop accused the authorities of Tombura State of mistreatment and torture of clergy and of making false accusations against the priest. Several priests were arrested at the same time, but were later released.
On 24th April 2018, a humanitarian worker employed by the Adventist Development and Relief Agency (ADRA) was killed by unknown gunmen who attacked his vehicle.
Endnotes / Sources
 ‘South Sudan president signs peace deal with rebels, Al Jazeera, 27th August 2015, https://www.aljazeera.com/news/2015/08/south-sudan-expected-sign-peace-deal-rebels-150826084550000.html (accessed 6th June 2018)
 ‘South Sudan expedites efforts to enact new constitution”, Sudan Tribune, 20th November 2017, http://www.sudantribune.com/spip.php?article64059 (accessed 7th May 2018).
‘JMEC chairperson lauds ‘significant progress’ on S. Sudan’s Constitutional amendment process’, Website Joint Monitoring and Evaluation Commission (JMEC) www.jmecsouthsudan.com, 21st November 2017, http://www.jmecsouthsudan.com/index.php/ncac-news/item/209-jmec-chairperson-welcomes-significant-progress-on-constitutional-amendment-process (accessed 7th May 2018).
 ‘Parliament to incorporate faltering peace deal into constitution’, Radio Tamazuj, 28th April 2018, https://radiotamazuj.org/en/news/article/parliament-to-incorporate-faltering-peace-deal-into-constitution (accessed 7th May 2018).
 ‘South Sudan – 2011 (rev.2013)’, The Constitute Project www.constituteproject.org, https://constituteproject.org/constitution/South_Sudan_2013?lang=en (accessed 7th May 2018).
 Bureau of Democracy, Human Rights and Labour, 2016 Report on International Religious Freedom – Southern Sudan, U.S. Department of State, http://www.state.gov/j/drl/rls/irf/religiousfreedom/index.htm?year=2016&dlid=268698 (accessed 29th April 2018).
 ‘High charges may force some radio stations to shut down in South Sudan’, Catholic Radio Network, 11th May 2018, http://catholicradionetwork.org/?q=node/27094 (accessed 12th May 2018).
 Kevin J. Kelley, ‘Volunteers in effort to count numbers of South Sudan war’, Daily Nation, 5th January 2018, https://www.nation.co.ke/news/africa/Volunteers-count-number-of-South-Sudan-war-dead/1066-4252426-msnho3z/index.html (accessed 11th May 2018).
 ‘UPDATED: Special investigation: 40 Church leaders killed in South Sudan since 2013’, Radio Tamazuj, 16th April 2017, https://radiotamazuj.org/en/news/article/special-investigation-39-church-leaders-killed-in-south-sudan-since-2013 (accessed 10th May 2018).
 “It also found that Government security forces, including the National Security Service, Sudan People’s Liberation Army, and the South Sudan National Police Service, were responsible for two-thirds of the verified cases of human rights violations.” Quoted in ‘New UN reports cites violations of rights of freedom of opinion and expression in South Sudan’, UN News, 22nd February 2018, https://news.un.org/en/story/2018/02/1003301 (accessed 11th May 2018).
 Some examples of this role of Church leaders denouncing injustices:
‘The bishops denounce: War crimes committed on the basis of ethnicity’, Agenzia Fides, 24th February 2017, http://www.fides.org/en/news/61808-AFRICA_SOUTH_SUDAN_The_Bishops_denounce_War_Crimes_committed_on_the_basis_of_ethnicity (accessed 12th May 2018).
‘Anglican archbishop accuses govt of failing to protect civilians’, Radio Tamazuj, 4th December 2017, https://radiotamazuj.org/en/news/article/anglican-archbishop-accuses-govt-of-failing-to-protect-citizens (accessed 10th May 2018).
‘South Sudan top religious leader says carelessness caused war’, Radio Tamazuj, 27th September 2016, https://radiotamazuj.org/en/news/article/south-sudan-top-religious-leader-says-carelessness-caused-war (accessed 10th May 2018).
 ‘The Auxiliary of Juba: No to National Prayer called by the President whose troops are responsible for the tragedy that afflicts us’, Agenzia Fides, 6th March 2017, http://www.fides.org/en/news/61872-AFRICA_SOUTH_SUDAN_The_Auxiliary_of_Juba_No_to_National_Prayer_called_by_the_President_whose_troops_are_responsible_for_the_tragedy_that_afflicts_us (accessed 12th May 2018).
 ‘Catholic radio in South Sudan harassed by security after airing ‘devils’ homily’, Radio Tamazuj, 5th July 2016, https://radiotamazuj.org/en/news/article/catholic-radio-in-south-sudan-harassed-by-security-after-airing-devils-homily (accessed 10th May 2018)
 ‘S. Sudan army accused of killing Mundri diocese priest’, Sudan Tribune, 18th October 2016, http://www.sudantribune.com/spip.php?article60581 (accessed 10th May 2018).
‘Breaking: SPLA kills a priest of the Episcopal Church of South Sudan’, Nyamile.com, 18th October 2016, http://nyamile.com/2016/10/18/breaking-spla-kills-a-priest-of-the-episcopal-church-of-south-sudan/ (accessed 10th May 2018).
 ‘Gbudue state authorities order Catholic Church’s closure’, Sudan Tribune, 24th January 2017 http://www.sudantribune.com/spip.php?article61479 (accessed 8th May 2018).
 ‘Catechist killed in Kajo-Keji clashes’, Radio Tamazuj, 25th January 2017, https://radiotamazuj.org/en/news/article/catechist-killed-in-kajo-keji-clashes (accessed 9th May 2018).
 Johnson Thembo, ‘South Sudan Episcopal Priest killed brutally killed in Yei town’, The Insider, 13th March 2017, http://theinsider.ug/index.php/2017/03/13/south-sudan-episcopal-priest-brutally-killed-in-yei-town/ (accessed 19th April 2018).
 ‘Unknown men kill priest in Mundri East County’, Radio Tamazuj, 30th March 2017, https://radiotamazuj.org/en/news/article/unknown-gunmen-kill-priest-in-mundri-east-county (accessed 9th May 2018).
 ‘Unknown gunmen kill priest in Tonj State’, Radio Tamazuj, 18th April 2017, https://radiotamazuj.org/en/news/article/unknown-gunmen-kills-priest-in-tonj-state (accessed 9th May 2018).
 ‘South Sudan denounces murder of Kenyan bishop’, Sudan Tribune, 25th June 2017, http://www.sudantribune.com/spip.php?article62832 (accessed 19th April 2018).
 ‘The coordinator of ‘Justice and Peace’ of the Diocese Wau arrested’. Agenzia Fides, 28th August 2017, http://www.fides.org/en/news/62811-AFRICA_SOUTH_SUDAN_The_coordinator_of_Justice_and_Peace_of_the_diocese_of_Wau_arrested (accessed 12th May 2018).
 ‘Kenyan priest threatened, deported from South Sudan’, La Croix, 5th February 2018, https://international.la-croix.com/news/kenyan-priest-threatened-deported-from-south-sudan/6869 (accessed 9th May 2018).
 The full letter is available at ‘Expulsion of Catholic missionary priest in South Sudan’, Sudan Google Group, 6th February 2018, https://groups.google.com/d/msg/sudans-john-ashworth/um-xlhqiOFc/NLsJILG3AwAJ (accessed 9th May 2018).
 ‘Aid worker killed in Terekeka State’, Radio Tamazuj, 1st May 2018, https://radiotamazuj.org/en/news/article/aid-worker-killed-in-terekeka-state (accessed 10th May 2018).