Amien Rais' activities in Muhammadiyah began in 1985 when he led The Council of Preacher (Majelis Tabligh).

Rais led ICMI's Expert Council, but resigned in 1997 under pressure from Suharto because he argued on the Busang and the Freeport cases.

In 1993, at a Muhammadiyah mid-term meeting (Tanwir) in Surabaya, Rais urged a presidential succession, a very rare issue amid the New Order regime.

Several days later, he invited some prominent Muslim figures – including Abdurrahman Wahid, Emha Ainun Najib, Nurcholish Madjid and Malik Fajar – to discuss the nation's current condition.

Suharto proposed to establish a Reform Committee, to reshuffle the cabinet ministers and to resign from the presidency within 6 months.

On 20 May, Amien Rais cancelled the mass rally to Monas square as an army general threatened to make "another Tiananmen" should he do so.

Amien Rais and other reformists established the National Mandate Party (Partai Amanat Nasional/PAN) on 6 August 1998.

PAN gained 6 percent of the vote in the 1999 election but failed to nominate Rais as a presidential candidate.

[13] Before leaving PAN, he was involved in internal rift with fellow party politicians over support for Jokowi's administration.

One of the founders of PAN, Abdillah Toha criticized him for his controversial statements and inconsistencies on many issues including his support on changing local elections to be indirect, and called him a "traitor of the Reform".

[16] In a corruption scandal trial of a former health minister, Siti Fadilah Supari, Amien Rais was reported to have received funds related the case.