Justice Darius Khobo ordered that the IMN leader be accompanied abroad by officials of the Kaduna State government, The Pulse reports.
The presiding judge ruled that El-Zakzaky and his wife should proceed to India for medical treatment.
He, however, did not give any time frame as to how long they will stay in India.
No date has been fixed for the defendants to embark on the medical trip.
Reacting to the ruling, counsel to the Kaduna State government, Dari Bayero, said the prosecution team would go back and study the judgement to see if there were grounds for appeal.
El-Zakzaky and his wife were arrested in Kaduna in 2015 after soldiers killed over 300 members of the IMN for allegedly throwing stones at the convoy of the Chief of Army Staff, Lieutenant-General Tukur Buratai, an act declared by the Army to be an assassination attempt.
Corporal Yakubu Dankaduna, a soldier, was allegedly killed by IMN members when he alighted from Buratai’s convoy to disperse the group’s procession during the confrontation.
The government ignored a December 2016 ruling of a Federal High Court to release them.