MPs from Khan's Pakistan Tehreek-e-Insaf party repeatedly chanted "Vote-thief!" as Shehbaz Sharif, who is expected to form the government, entered the lower house of parliament on Thursday with his brother Nawaz Sharif.
Both men are former prime ministers.
The house echoed with chants of "Long Live Sharif!" when the brothers signed the register after taking their oaths of office.
Bilawal Bhutto Zardari, the young chairman of the Pakistan People's Party and a key Sharif ally, was met with similar chants.
Muslim League-N party members hold posters of leaders Nawaz Sharif and Shahbaz Sharif. (AP PHOTO)
The new government will face challenges including a surge in militant attacks and shortages of energy; as well as an ailing economy that will force Pakistan to seek another bailout from the International Monetary Fund.
MPs from Khan's PTI told reporters that they will continue their campaign against the rigging in the elections in and outside the parliament.
"Yes, the election has been rigged," said Gohar Ali Khan, the head of PTI.
PTI has called for nationwide rallies on Saturday.
The party claims it results were changed in dozens of constituencies to prevent it from winning a majority, a charge the Election Commission of Pakistan denies.
After the February 8 elections, observers from the Commonwealth praised election officials for holding the vote despite multiple militant attacks, but the US State Department said that the vote was held under restrictions of freedoms of expression, association and peaceful assembly.
The European Union also criticised the inability of some political actors to contest the elections.
Pakistan's foreign ministry has fired back at such criticism, saying the vote was held in a free, fair and transparent manner.
None of the foreign observers described widespread vote-stealing.
Sharif's Pakistan Muslim League party, or PML-N, and Pakistan People's Party of former President Asif Ali Zardari, emerged from the vote as the largest presence in the 336-seat National Assembly, or lower house of the parliament.
Under a power-sharing formula, Sharif's party will support Zardari in next month's presidential elections. Outgoing President Arif Alvi is an ally of Khan and was a senior member of PTI before becoming president.
Khan is serving prison terms in multiple cases and has been barred from seeking or holding office.
He has been convicted on charges of corruption, revealing official secrets and violating marriage laws in three separate verdicts and sentenced to concurrent prison terms of 10, 14 and 7 years.
Khan is appealing all the convictions and still faces some 170 legal cases on charges ranging from corruption to inciting violence and terrorism.
