But before even half the votes were counted, Khan's leading rival, Shahbaz Sharif, who heads the Pakistan Muslim League, the party of jailed ex-prime minister Nawaz Sharif rejected the vote, generating fears that disgruntled losers could delay the formation of the next government. The results had been expected by 2 a.m. local time.
The third major party, the Pakistan Peoples Party, also complained that its polling agents were asked to leave during the vote count in a number of voting centers.
In Bani Gala, a suburb of the capital Islamabad, media massed outside the polling station where Khan is due to cast his vote.
The PML-N, on the other hand, says it is the target of the alleged military machinations, with candidates under pressure and Nawaz Sharif ousted from power previous year and jailed over a corruption conviction days before the vote, removing Khan's most unsafe foe from the race. "The way the people's mandate has blatantly been insulted, it is intolerable", Shehbaz, PML-N president and Nawaz Sharif's brother, told a news conference.
"There's no conspiracy, nor any pressure in delay of the results".
By Thursday partial, unofficial results gave him at least 100 seats so far in the National Assembly, the lower house.
In Punjab, the country's most populous province and political power base, PML-N stands ahead of PTI with 51 percent votes; however, PTI, which enjoys the support of 31 percent votes, is quickly gaining ground, the surveys conducted by think tanks, Gallup Pakistan and Pulse, revealed.
Pakistanis started casting votes in the country's one-day general elections commenced on Wednesday morning, which would elect the members of the National Assembly, the lower house of the country's parliament, and of the four provincial assemblies.
But, there have been widespread concerns during the election campaign about manipulation by the military, which has directly or indirectly ruled Pakistan for most of its existence. Nawaz Sharif was ousted from power previous year and jailed over a corruption conviction days before the vote, removing Khan's most unsafe rival.
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His party would need to win 141 of 272 seats to form a government on its own but would be more likely to form a governing coalition with other parties.
"The overwhelming sentiment in favor of PTI all over the country proves that the people of Pakistan now want IK as their leader and PTI as the party in power to bring about the much needed change this country has been waiting for", Haque said in an earlier statement.
"It is a sheer rigging".
"We totally reject this result", he said.
Khan's party spokesman, Fawad Chaudhry, showed confidence as the early projections were broadcast, saying in a tweet "Congratulations to the nation on a new Pakistan!"
Though considered as Pakistani military's favourite son, Khan campaigned immensely against corruption and with a promise to reform systems within the government.
Ex-chief minister Pervez Khattak, who won the NA-25 (Nowshera) seat, was also leading in two provincial assembly constituencies in his native Nowshera.
In Punjab, with results from 19 per cent polling stations available with ECP, PML-N is now leading the race with 137 provincial seats but PTI is closing in with 115 seats.
The countrywide election campaign, marred by a string of terrorist attacks, came to an end on Monday night, as political parties culminated their poll campaigns. It's an incredible lesson in tenacity, belief and refusal to accept defeat.