They shouted slogans against the slain Mashal Khan and vowed to challenge the decision of ATC at the Supreme Court.
Twenty-five accused in the case were awarded sentences of four years each, while 26 suspects were acquitted by the court for lack of evidence.
During the trial Imran Ali pleaded guilty to shooting Mashal Khan.
An initial investigation after the incident, which shocked the country and sparked global condemnation including from the United Nations, found that blasphemy accusations against Mashal Khan were unfounded, and that he was mercilessly beaten and killed for being vocal against irregularities at his university, including on a local television programme.
Some of the 50 people providing testimony to the court said the victim had angered the university administration by criticising their management of the institution.
After a few months Mashal Khan's case investigation proved that he was falsely accused by some secular students group who were afraid of his criticism on rising fees and corruption at university.
Warning the government against challenging the acquittal, he said the appeal against acquittals "will hurt the sentiments of Muslims" that may "may spark protests across the country".
Mashal Khan was accused of blasphemy, beaten and finally shot by a mob.
While the judge was preparing to announce the judgement, relatives of the accused were found protesting outside the court. The court sentenced life imprisonment to the other five men for murdering the student.
The protest sponsored by the Jamaat-e-Islami (JI), Jamiat Ulema-e-Islam-Fazl (JUI-F) and Maulana Samiul Haq's Jamiat Ulema-e-Islam (JUI-S) will be held after Friday prayers at a mosque in Mardan, under the banner of "Khatm-i-Nabuwwat Mardan".
The JI is also holding a gathering in Mardan on Thursday (today) to "welcome" those acquitted by the ATC. People all over Pakistan protested against that brutal murder.
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