He moved to Java to pursue higher education, becoming active in Islamic student organizations and enrolling in the Rechts Hogeschool in Batavia (now Jakarta) before his studies were interrupted by the Japanese invasion in 1942.

After the downfall of Prime Minister Ali Sastroamidjojo's first cabinet, he was given another chance and formed a caretaker government with the Nahdlatul Ulama (NU) and several minor political parties.

Burhanuddin was born in Medan on 12 February 1917,[a] the second child of Mohammad Yunus, a low-ranking official in a public prosecutor's office, and his wife Siti Nurfiah.

He continued his education at the Rechts Hogeschool (Batavia Law Institute), but his studies were interrupted by the Japanese invasion of the Dutch East Indies in 1942.

[2][9] Along with Jusuf Wibisono and Mohammad Roem, Burhanuddin organized the publication of the Dutch-language journal Moslim Reveil espousing Indonesian Islamic nationalism.

[14] Burhanuddin also contributed to the collapse of the cabinet later that year, when he threatened to withdraw Masyumi's support for the government over a successful motion to establish formal diplomatic relations with the Soviet Union.

[15] After the collapse of Wilopo's cabinet, two initial attempts at forming a new government by PNI and Masyumi failed, and after a series of negotiations between the two parties Burhanuddin was appointed formateur by President Sukarno on 8 July 1953.

[17] His succeeding formateur, Wongsonegoro of the Great Indonesia Unity Party, managed to organize the First Ali Sastroamidjojo Cabinet which excluded Masyumi from ministerial posts.

[24] It was intended that the cabinet would return its mandate after the upcoming elections had concluded, effectively making it a caretaker government and limiting its ability to influence long-term policy.

[26] In addition to changes in the bureaucratic structure and personnel, Burhanuddin also called for another general amnesty for members of the Darul Islam rebellion in West Java.

[29] Despite NU and PSII also being Islamist parties, they had a significantly different support base to Masyumi,[e] and resisted many of the proposed changes to the bureaucratic and economic structures of the country.

[31] In the weeks leading up to the 1955 election, the cabinet also made several populist policies, including reducing petrol prices by nearly half and simplifying import regulations.

As a result of the shifting balance of political power, Masyumi opted to back out from supporting an anticorruption bill in parliament, which could have antagonized the NU and received a presidential veto.

[36][37] Under NU pressure, Burhanuddin also agreed to appoint Abdul Haris Nasution – who had previously lost his post due to the 17 October affair in 1952 – back to his old position as army chief of staff.

[5] Even with the changed political situation, Burhanuddin's cabinet continued to remove PNI and PKI-supporting personnel from civilian and military offices alike – at the cost of reduced performance of the ministries.

[39] An incident in December 1955 where Burhanuddin attempted to appoint an officer, Sujono, to the Indonesian Air Force high command resulted in the resignation of its chief of staff Soerjadi Soerjadarma.

[40] Burhanuddin's cabinet engaged in rationalization efforts, reversing the economic policies of PNI in favor of a pragmatic approach that welcomed foreign and private capital into Indonesia.

[43] Burhanuddin's cabinet also abolished the pro-indigenous Benteng program and unilaterally abrogated the Dutch–Indonesian Round Table Conference – specifically, Indonesia's remaining debt obligations exceeding 3 billion guilders.

[45] In foreign policy, the Burhanuddin cabinet aimed to placate the concerns of the United States about Indonesia's relations with the communist bloc to gain American support in the Western New Guinea dispute.

[49] After the election, despite opposition from Sukarno and PNI, Burhanuddin continued with negotiations,[50] which resulted in the withdrawal of NU and PSII ministers from the government in late January 1956.

[60][61] Burhanuddin and other Masyumi leaders were especially in the spotlight, due to his cabinet's economic policy which was perceived to have benefited foreign importers and Chinese Indonesians.

Indonesian newspapers began to attack the three figures, and rumors spread that they had been killed or arrested – some of Burhanuddin's family members travelled from Sumatra to Jakarta, believing that he had died.

[60][63] Under the auspices of visiting a friend, Burhanuddin was in Padang in mid-January 1958, and along with other Masyumi leaders, he attended a conference at the town of Sungai Dareh with dissident military officers.

[68][69] Burhanuddin later claimed that he was not fully in favor of forming a rival government, that he had only agreed to be appointed minister of home affairs simply so there could be a cabinet, and that the military officers had reassigned him without consultation.

[72][73] PRRI soon was forced into guerilla warfare, with Burhanuddin being attached to Dahlan Djambek's northern sector based in Agam Regency.

[74] Due to continued government military pressure, however, they were soon dislodged from their bases there and into the jungles and mountains of Sumatra, with the final major PRRI stronghold of Koto Tinggi [id] being taken in July 1960.

Along with Sjafruddin and Assaat, Burhanuddin first called for PRRI forces to cease hostilities against the Indonesian government, before surrendering to military authorities at Padangsidempuan in late August 1961.