On January 16, 1962, at 4 a.m., Sjahrir was arrested at his residence on Jalan Jawa no. 61 (now Jl. H.O.S. Cokroaminoto). Other figures were Anak Agung Gde Agung, Soebadio Sastrosatomo, and Sultan Hamid II. The detained Masjumi figures were Prawoto Mangkusasmito, Yunan Nasution, Kiai H. Isa Anshary, and Moh. Rom.
Sjahrir and other political prisoners were initially held in the Military Dormitory on Jalan Hayam Wuruk, Central Jakarta. Then moved to a house on Jalan Daha, Kebayoran Baru, South Jakarta. Three months later, they were transferred to the prison in Madiun, where they were placed in a military detention center on Jalan Wilis. While serving his prison term in Madiun, Sjahrir spent most of his time reading books and writing down things that worried him.
1962, Sjahrir suffered from high blood pressure after undergoing treatment at the Gatot Subroto Army Hospital. Then, he was transferred to the prison in Jalan Kegungan from 1963 to 1964. Then, in February 1965, he was transferred to the Military Detention Center (RTM) on Jalan Budi Utomo.
One night, Sjahrir fainted due to a stroke but did not immediately receive medical help. Only the next day, he was rushed to hospital; after surgery, it turned out that Sjahrir could no longer speak. His wife tried to get him to seek treatment abroad. President Seokarno allowed him to seek treatment abroad but he remained a prisoner. The President allowed Sjahrir to seek treatment anywhere except the Netherlands. On July 21, 1965, Sjahrir, his wife, and two children departed from Kemayoran airport for Zurich, Switzerland.
Doctors in Zurich could not cure Sjahrir, and he suffered bleeding on the brain. For seven days, he was in a coma. On April 9, 1966, he died peacefully at the age of 57 years. On April 15, 1966, Indonesian radio, press, and television broadcast a decree signed by President Soekarno, an order dated when Sjahrir died; the rule declared Sjahrir a National Hero. His body was returned to Indonesia and arrived on April 17.