Sisi, a former army chief who won elections after toppling his Islamist predecessor Mohamed Morsi in 2013, had promised to look into pardoning prisoners at a youths' conference last month.
The pardoned include Islam al-Behairy, a television show host and Islamic reform advocate sentenced to a year in prison for criticising canonical religious works, presidency spokesman Alaa Youssef told AFP.
Nashwa el-Hofy, a member of a panel that recommended prisoners for the pardons, said the focus was on "university youths".
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"We focused on those who have a final ruling against them," she said.
Sisi has also pledged that the government would look into revising a protest law that bans all but police sanctioned demonstrations.
Morsi's overthrow in July 2013 unleashed a crackdown on his supporters that killed hundreds of protesters and jailed thousands.
The crackdown extended to liberal and leftwing activists who had supported Morsi's ouster but turned against the government after rights abuses mounted.
Sisi pardoned 100 people in September 2015, including two journalists and several prominent dissidents.