Together with the priest Nikolai Eschliman, Yakunin wrote an open letter in 1965 to the Patriarch of Moscow, Alexius I, where he argued that the Church must be liberated from the total control of the Soviet state.

In 1990 Yakunin was elected to the Supreme Soviet of the Russian Federation and worked as deputy chairman the Parliamentary Committee for the Freedom of Conscience.

Gleb Yakunin was a member of the committee created for the investigation of the Soviet coup attempt of 1991 and chaired by Lev Ponomaryov, and thereby gained the access to secret KGB archives.

He published code names of several KGB agents who held high-rank positions in the Russian Orthodox Church including Patriarch Alexius II, Metropolitans Filaret of Kyiv, Pitrim of Volokolamsk, and others.

He criticized the law "On Freedom of Conscience and Religious Associations" adopted by the Duma[3][4] and made numerous statements in support of human rights in Russia.

[5] As is traditional for Orthodox parish priests, Gleb Yakunin was married, and had three children: Maria, Alexander and Anna.