Khan was administered the oath of office by Chief Justice Nasirul Mulk in a special ceremony held at the Supreme Court.
He was appointed by the special parliamentary committee on Thursday after the government referred three names to it for choosing the Chief Election Commissioner (CEC).
The office of CEC was vacant for over 16 months as government and opposition failed to agree on a single name as required under the law.
The final push for appointment came from the Supreme Court which set December 5 as deadline for the appointment and threatened to issue notice to Prime Minister Nawaz Sharif and opposition leader Khursheed Shah.
The new CEC enjoys the support and confidence of all political parties.
Khan was born in 1945 in Namli Maira in Abbottabad district and did an MA in economics and an LLB degree from the Punjab University, News agency reported.
He became a civil judge in 1968 and an additional judge for two years in 1993, before taking permanent office at the Peshawar High Court.
He was appointed Chief Justice of the Peshawar High Court in 2000 and two years later became a judge at the Supreme Court.
After refusing to take oath under the Provisional Constitutional Order (PCO) on November 3, 2007, he was removed from the Supreme Court following the imposition of emergency by then military ruler Pervez Musharraf.
He was reinstated to the court under the democratically- elected government which came to power in 2008. He retired from the Supreme Court of Pakistan in 2010.
Later, he was appointed as chief justice of the Federal Shariat Court but he resigned from the post yesterday after being named as the new CEC.