Mousa said he would mount a full challenge to Sissi, though opposition activists, journalists and analysts took to Twitter to dismiss him as a dummy candidate, standing only to give the impression of a full democratic contest.
"This is all theater," said a shopkeeper outside the Ghad Party headquarters in downtown Cairo.
Sissi was elected in 2014, a year after leading the army to oust President Mohamed Morsi, an Islamist.
This is the third election since protests in 2011 unseated longtime ruler Hosni Mubarak.
Several leading opposition figures have called for a boycott of the election, slated for March 26-28, saying repression has cleared the field of challengers and left Sissi's top opponent in jail.
Even before campaigning has officially begun, the United Nations, rights groups and opposition figures have criticized the run-up as compromised by arrests, intimidation of opponents and a nomination process stacked in favor of the incumbent.
At a news conference, Mousa said the late decision to run came after all other candidates withdrew. He dismissed accusations that his candidacy was being used to present a false sense of competition.
"We are entering a fair and honorable competition in order to win," Mousa said.
The electoral commission has said it will ensure that the vote is fair and transparent.
Would-be candidates were required to register by 2 p.m. Monday after clinching at least 20 nominations from parliament or 25,000 pledges from residents across the country.
Mousa submitted his official paperwork just minutes before the deadline. He said he had netted more than 47,000 pledges and the backing of 27 lawmakers.
Sissi's campaign said Monday that it had received nomination pledges from 915,000 residents. More than 500 of parliament's 596 lawmakers had already pledged support for Sissi.
"We have a respectable program that we are offering to the Egyptian people, and we are presenting ourselves just like any other candidate would," said the deputy head of the Ghad party, Mahmoud Mousa.
Over the weekend, Hisham Genena, a former anti-corruption watchdog chief who had been working to elect former military chief of staff Sami Anan, was attacked and badly wounded outside his home.