Egypt's military said they had carried out air strikes and raids overnight against militants held responsible for the killings, the bloodiest attack in Egypt's modern history.
The attack also left 128 people injured, the MENA state news agency reported, while Egypt's public prosecutor's office linked it to ISIS terrorists, also known as Daesh.
"They numbered between 25 and 30, carrying the Daesh flag and took up positions in front of the mosque door and its 12 windows with automatic rifles," the prosecutor said in a statement.
The gunmen, some wearing masks and military-style uniforms, surrounded the mosque blocking windows and a doorway and opened fire inside with automatic rifles, the statement said, citing their investigation and interviews with wounded survivors.
No group has claimed responsibility, but Egyptian forces are battling a stubborn ISIS affiliate in the region, one of the surviving branches of the militant group after it suffered defeats by US-backed forces in Iraq and Syria.
"The air force has over the past few hours eliminated a number of outposts used by terrorist elements," the army said.
Witnesses say gunmen set off a bomb at the end of Friday prayers at the Al Rawdah mosque in Bir al-Abed, west of El-Arish city, and then opened fire as worshippers tried to flee, shooting at ambulances and setting fire to cars to block roads.
Images on state media showed bloodied victims and bodies covered in blankets inside the mosque.
Striking a mosque would be a shift in tactics for the Sinai terrorists, who have previously attacked troops and police and more recently tried to spread their insurgency to the mainland by hitting Christian churches and pilgrims.
Local sources said some of the worshippers were Sufis, whom groups such as ISIS consider targets because they revere saints and shrines, which for hardliners is tantamount to idolatry. ISIS has targeted Sufi and Shi'ite Muslims in other countries like Iraq.
The jihadists in Egypt's Sinai have also attacked local tribes and their militias for working with the army and police.
Sisi, a former armed forces commander who supporters see as a bulwark against terrorists, promised the "utmost force" against those responsible for Friday's attack. Security has been a key reason for his supporters to back him, and he is expected to run for re-election next year.
"What is happening is an attempt to stop us from our efforts in the fight against terrorism," he said on Friday.
North Sinai, a mostly desert area which stretches from the Suez Canal eastwards to the Gaza Strip and Israel, has long been a security headache for Egypt and is a strategic region for Cairo because of its sensitive borders.
Local militant group Ansar Bayt al-Maqdis, once allied to al Qaeda, split from it and declared allegiance to ISIS in 2014. But attacks in the Sinai worsened after 2013 when Sisi led the overthrow of President Mohamed Mursi of the Muslim Brotherhood after mass protests against his rule.