The men were charged with "illegal gathering" in relation to violence in Cairo on August 16 last year, two days after the security forces killed hundreds of Morsi supporters while breaking up their protest camps in the capital.
Of those charged, 117 were still being held. They will now be freed. Others charged in the case had already been released. Further details on the ruling were not immediately available.
The authorities have jailed thousands of Morsi supporters since the army deposed the Brotherhood politician last July following mass protests against his rule.
Earlier this year, a judge issued preliminary death sentences against 1,200 Brotherhood supporters and members in two separate cases, triggering heavy condemnation from human rights groups. The convicted included the group's leader, Mohamed Badie.
Rights groups criticized the trials for deep procedural flaws, and despite the acquittals, other courts are continuing with convictions.
A judge in Alexandria on Monday convicted 62 people and sentenced them to jail terms of up to 25 years in relation to political violence last July. The judge also upheld the death penalty against one of those charged in the case.
This came a day after more than 160 Brotherhood supporters were handed sentences of up to 15 years in prison.
RA/NJF