Elections were held on May 7 in Lower Dir region in the conservative province in the northwest and won by a candidate of right-wing Islamic party, Jamat-i-Islami.
Local media and civil society groups said that women were absent from the polling station as they were barred under an agreement by political parties and elders.
The Election Commission of Pakistan (ECP), which supervises the polls, after a meeting yesterday cancelled the results and ordered re-polling in the constituency.
"New election schedule shall be announced in accordance with law, in due course," it said.
Aizaz-ul-Mulk who had won the elections criticised the ECP and said that no agreement was made to stop women from voting. He decided to challenge it in the Supreme Court.
Women in conservative north-western region are often not allowed to go out of their homes and often barred to vote for which they need to go out to the polling stations.