He was born on 20 March 1981 in Paniala, in the Dera Ismail Khan district in Pakistan's North West Frontier Province into an ethnic Pashtun family.

[8] At the 2006 FIFA World Cup qualification in November 2003 against Kyrgyzstan, Khan replaced Haroon Yousaf as the captain of the national team.

[9] After playing at the 2004 Summer Olympics qualifiers, he took the under-23 side all the way to the final of the 2004 South Asian Games against India, where his string of saves gave Pakistan a 1–0 victory.

[12] In December 2009, at the end of the SAFF Championship in Bangladesh, Jaffar publicly stated his decision to retire from international football after a fallout with Pakistan's Austrian coach György Kottán,[13] but returned later on captaining the under-23 side at the 2010 Asian Games.

At the 2011 SAFF Championship, he conceded a single goal in the three matches all resulting in a draw, failing to register the qualification for the semifinal round.

After a series of friendlies against Singapore, Nepal and Maldives in 2012 and 2013, he played his last match for the national team against Macau at the 2014 AFC Challenge Cup qualification.

He was ruled out of the 2013 SAFF Championship due to knee injury during a match of the Inter-Services Football tournament at the Naval Sports Complex.