Morsi's speech Wednesday marked a first in decades for a sitting Egyptian head of state at the U.N. General Assembly.
He said the crisis in Syria was one that weighed "heavily" on the minds of members of the international community.
"The bloodshed in Syria and the humanitarian crisis that has unfolded, must be stopped," he said.
Morsi told a summit for the Non-Aligned Movement in Iran last month that Syrian President Bashar Assad has lost legitimacy to lead because of the civil war in the country. The Egyptian president told the United Nations he supported a new regime in Damascus.
"We will continue to work to put an end to the suffering of the Syrian people and provide them an opportunity to choose freely the regime that best represents them," he said in his prepared remarks.
The U.N. Security Council has been unable to reach a consensus on Syria because of concerns by Russia and China that resolutions lacked balance. By U.N. estimates, at least 18,000 people, mostly civilians, have died as a result of the conflict that began in March 2011.
Rebel fighters attacked a military facility in Damascus Wednesday, their second attack on a Syrian military facility in the capital in two days.