The Islamic group, which is also known as Shiite Movement, has a large followership across the country.
El-Zakzaky spoke with a select group of journalists at the office of the Department of State Services in Abuja on Saturday.
It was his first appearance after two years of his arrest by the army following the clash between his followers and soldiers in Kaduna, Kaduna State, in December 2015.
The meeting between him and journalists lasted for one minute and 20-seconds
Dressed in a white flowing gown with a turban and a pair of glasses, El-Zakzaky thanked Nigerians for their prayers.
He also thanked the DSS for allowing him access to his doctors, saying he was seriously sick last Monday.
He, however, said that his health condition had improved.