It was not immediately clear whether the pardons, reported by state television, included prominent Arab Spring activists such as Ahmed Maher and Alaa Abdel Fattah.
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.
Nashwa el-Hofy, a member of a panel that recommended prisoners for the pardons, said the focus was on "university youths".
"We focused on those who have a final ruling against them," she said.
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.
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