The protest started from the Wuse Market to the Federal Secretariat in Abuja.
El-Zakzaky has remained in detention since he was arrested in December 2015, following a clampdown on his members by soldiers.
Over 300 Shi’ites were killed during the onslaught by soldiers who accused the Shi’ites, members of the Islamic Movement of Nigeria, of blocking a road being used by the army chief, Tukur Buratai. A soldier was also killed in the violence.
After his detention, the federal government failed to file formal charges against Mr El-Zakzaky but rather appealed a December 2016 order for his release.
Following the inability of government to release El-Zakzaky, Shi’ite members began a daily protest in Abuja and parts of the north.
This forced the government to file a formal charge against Mr El-Zakzaky in April, over two years after he was detained.
The Shi’ite leader and his wife were later arraigned on an eight-count charge for alleged homicide.
On Friday, the Shi’ites took to the streets of Abuja brandishing pictures of their members, whom they claimed had been killed by security operatives during past protests.
Past Shi’ite protests have resulted in clashes between them and the police. Friday’s protest was violence free.
In a telephone interview with Premium Times, a human rights lawyer, Femi Falana, said the continued detention of Mr El-Zakzaky and his wife “is the height of official impunity”.
According to Mr Falana, “this is the first time that a man and his wife have been detained for security reasons by any regime since the creation of Nigeria in 1914.
“As President Buhari has publicly embraced the rule of law, I am compelled to demand for the release of the couple in line with the valid and subsisting orders of the federal high court made on December 2, 2016,” Mr Falana added.
Similarly, a follower of El- Zakzaky, Abdullahi Musa said: “Sheikh El- Zakzaky has spent 1000 days in an unjust detention by the government despite the court ruling that ordered for his release and compensation”.
According to Musa, their leader has serious health challenges.
“The Sheikh has over millions of followers, if by chance he dies while in detention, the presidency should be ready to face the consequences,” Musa said.