He and his wife, Zeenat, departed Nnamdi Azikiwe International Airport, Abuja, alongside some family members and security operatives.
The sheikh, who wore a nose mask, occupied a first-class seat.
Officials of the National Intelligence Agency (NIA) and Department of State Services (DSS) were reported to be with the IMN leader, which is one of the conditions of the medical leave granted by a high court in Kaduna.
The court had ruled that El-Zakzaky, who has been in detention since 2015, must return after his discharge from the hospital to face his charges.
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