The polling started at 10.00 a.m. amidst strict security arrangements at the National Assembly, the four provincial assemblies and the Senate.
The voting will continue without any break till 3.00 p.m.
Mamnoon Hussain, the India-born nominee of ruling PML-N, is likely to win the elections for the 12th President in the one-on-one contest with ex-judge Wajihuddin Ahmad of Pakistan Tehreek-i-Insaf party.
The main opposition party in the National Assembly, the Pakistan Peoples Party, had withdrawn its candidate and announced a boycott of the election over reservations on the decision of the Supreme Court to reschedule the poll.
More than 1,000 federal and provincial lawmakers are eligible to vote as they are part of the electoral college comprising federal parliament and four provincial assemblies.
After the completion of the poll, the ballots will be counted today and informal results will be announced by the evening. The formal notification of the winning candidate will be issued by the election commission of Pakistan.
The office of the president is ceremonial in Pakistan but he is still the constitutional chief of the armed forces.
Though, he cannot order deployments. He also appoints the services chiefs at the recommendation of the prime minister.
Pakistan so far had 11 presidents, out of which five were military generals. Four of them illegally got powers through coups, whereas first president Major Sikandar Mirza was elected in 1956 after the first constitution was adopted.