Sheikh Zakzaky and his wife departed on Monday from Abuja's international airport for New Delhi to receive medical treatment there.
The top cleric was last week granted bail by a court in Kaduna state in order to seek treatment abroad.
Sheikh Zakzaky has been held in detention since December 2015 and was charged just in April 2018 with murder, culpable homicide, unlawful assembly, disruption of public peace and other accusations. He has pleaded not guilty.
In 2016, Nigeria’s federal high court ordered his unconditional release from jail following a trial, but the government has so far refused to set him free.
The top cleric has lost his left eyesight in a raid by the Nigerian army on his residence in the northern town of Zaria in December 2015.
During the raid, Zakzaky’s wife sustained serious wounds too and more than 300 of his followers and three of his sons were killed. Zakzaky, his wife, and a large number of the cleric’s followers have since been in custody.