In 1989, he became the minister of education under then President Hashemi Rafsanjani and served until 1997.In 1997, he was appointed vice president and head of the Planning and Budget Organization by President Mohammad Khatami, but after a merge of the organization with another he was succeeded by Mohammad Reza Aref in the post. Najafi was an advisor to President Khatami and the senior advisor to the minister of industries from 2001 to 2005.