Mousavi Khoeini started his political career as an activist in the Islamic Students Association of Khajeh Nasir University.

He was later elected to be a member of Adver Tahkim Vahdat, a representative body of Islamic Students Associations in Iran.

Mousavi Khomeini also helped form a committee in the parliament to visit the prisons and report on the condition of the imprisoned activists.

Additionally, he tried to provide ways of financial support for the families of imprisoned political activists.

He was arrested during this protest on June 12, 2006, in Haft-e Tir Square in Tehran and was put in solitary confinement.