The Muslim Brotherhood last week nominated former financier Khairat al-Shater as the presidential candidate for its Freedom and Justice Party.
The Muslim Brotherhood, in a statement, said it was wary of "contrived hindrances" to democratic reform in Egypt.
"We, the Muslim Brotherhood and the FJP have, therefore, decided to nominate Dr. Mohamed Morsi, FJP Chairman as a second candidate for the presidency, as a necessary precaution to ensure the continuation of the march of the desired peaceful transition in this homeland," the statement read.
The Muslim Brotherhood took 20 percent of the parliamentary seats in 2005 elections by running as independent candidates. It was wiped off the political map during the last election before the country's 2011 revolution, however. FJP now holds a significant number of parliamentary seats.
Omar Suleiman, the country's former vice president and intelligence chief, entered the race last week alongside Shater and former Arab League Secretary-General Amr Moussa.
Presidential elections in Egypt are scheduled for May.