The earliest record of the presence of the Society of Jesus in Timor-Leste was at the end of the 19^th Century. In 1897, after Father António Antunes, a secular clergyman, established a Missão de Soibada, two Jesuits, Fr Sebastião Maria Aparício da Silva and Fr Manuel Fernandes Ferreira, were entrusted with the task of constructing the Church and their residence. Construction of the Church of Sagrado Coração de Jesus and the residence in Soibada began in 1900, and both were completed in 1904.  The mission also ran Colégio Nuno Alvares, a school for boys.  The new mission was to be short-lived as in 1910, all Religious, including the Jesuits, had to leave Timor-Portugues when the mandate for the Expulsion of all Religious Orders in all the Portuguese colonies was issued in Lisbon.

Upon their return to Timor-Portugues after some decades of absence, the Jesuits resumed their work in education and formation, especially of the future leaders of the Church. They ran the Pre-Seminário de St Francisco Xavier in Dare and Seminário Menor de Nossa Senhora de Fátima in Lahane until 2000, when the running of the seminary was turned over to the priests of the Diocese of Dili.

However, they continued to run Colégio de São José, a secondary school they had been entrusted with by the Diocese of Dili in 1993.  The Jesuits ran the school for 18 years before handing it back to the Diocese in December 2011.

It was around this time that the Society of Jesus made the decision to establish an ambitious education project in Timor-Leste. The Projeto Educação Jesuíta comprises a secondary school, Colégio Santo Inácio de Loiolá, and a teacher education institute, Instituto São João de Brito, in Kasait, a rural area about an hour’s drive from Dili. In 2013, Colégio de Santo Inácio de Loiolá opened with its first intake of Year 7 students, and Colégio de São João de Brito took its first intake of senior secondary school teacher trainees in January 2016.

In addition to the education project, the Society of Jesus has ventured over the years into various spiritual, pastoral, and social works. The Jesuits run a mission parish in Railaco with a church, secondary school, and health-care and regular feeding programs. Through Casa de Produção Audiovisual, an audio-visual production house, they help build the Timorese identity as an independent people and country, and foster a culture of peaceful dialogue, discussion, and active participation. In 2014, Jesuit Social Service Timor-Leste was established to offer programs and services to develop and empower communities, and build resilience in them through volunteerism, network building and partnerships.

The Jesuit Region of Timor-Leste is mainly composed of missionaries as the majority of the local Timorese Jesuits are young and still in formation. As they continue to serve the people of Timor-Leste, the Jesuits are keenly aware of the realities faced by the people and their living conditions. They were with the people when the country was in conflict and war, producing martyrs of freedom and faith Fr Tarcisius Dewanto SJ and Fr Karl Albrecht SJ, killed in September 1999; and they continue to be with the people as they work with them to alleviate poverty and provide some of the basic necessities and skills needed for nation and community building.