Khan received 176 votes in the 342-seat National Assembly, said Asad Qaiser, the speaker of the parliament. Rival candidate, Shehbaz Sharif of Pakistan Muslim League-Nawaz (PMLN), garnered 96 votes.
Khan’s Pakistan Tehreek-i-Insaf (PTI) party swept to power in the July 25 election but will need support from independents and smaller parties because it does not have enough seats in parliament to form a majority government.
Opposition parties have claimed elements of the elections were rigged, but they agreed to take their seats in the assembly.
In the lead-up to the election, Khan was widely seen as the favoured candidate of the “powerful” military, which was accused of meddling against his rivals.
Three-time Prime Minister Nawaz Sharif was ousted from office in 2017 over corruption allegations.
He was jailed in the lead-up to the vote, and his brother, Shahbaz Sharif, led the PML-N party into the election.
After the election, three major opposition parties banded together to nominate Shahbaz Sharif as a joint candidate in a bid to thwart Khan.
However, one of the parties – the PPP party of assassinated ex-Prime Minister Benazir Bhutto – is now reported to have decided to abstain from the vote.
The PPP and PML-N have dominated Pakistani politics for decades, governing several times in between periods of military rule.