After spending his youth career at the Tata Football Academy Khabra joined Sporting Clube de Goa in the I-League for which he scored two goals in his debut match while playing the IFA Shield against Army XI in 2006. In 2006 Khabra again scored in the Federation Cup finals which was the only goal for Sporting Clube de Goa against Mohan Bagan. In the same year 2006Durand Cup Khabra was awarded the promising player award. He scored one goal for on 15 November 2008 against East Bengal which would turn out to be Sporting's only goal of the game as the club lost 3–1 on the day. Khabra made a total of 24 assists while playing for Sporting Goa.
East Bengal
On 30 April 2009 it was announced that Khabra had signed with fellow I-League side East Bengal. On 10 November 2012 Khabra scored his first league goal for East Bengal against Air India in which he also scored a second goal as East Bengal won 3–0, he was awarded man. On 9 December 2012 Khabra became the hero of the East Bengal Club by scoring a sensational goal through header in the 43rd minute in the local derby against Mohan Bagan, unfortunately the match was abandoned though East Bengal was leading by 3-0 in front of 100,000 audience. Khabra became East Bengal's vice captain and said after this appointment that he is targeting to score more goals regularly and hopes that it will help him to earn a place in Indian Football Team. On 8 July 2014, he was appointed as the new captain of the club. Khabra has made a total of 39 assists as of 10 September 2014 for East Bengal. On 15 December 2013 Khabra was awarded as Man of the Match while playing against Bengaluru FC as Captain for East Bengal in the I-League fixture.
On 22 July 2014 Khabra joined the Indian Super League in the Domestic Player draft after being loaned from East Bengal and was the first pick in the 2014 ISL Inaugural Domestic Draft by Chennaiyin. He plays for Chennaiyin with Jersey Number 18 along with football legends such as Marco Materazzi, Elano, Mikael Silvestre, Bernard Mendy in the same team. On 21 October 2014 while playing against Kerala Blasters Khabra made the most important assist for Bernard Mendy and Mendy scored a fantastic bicycle kick goal out of this assist. On 29 October 2014 while playing against Mumbai City FC Khabra again created a good assist for Stiven Mendoza through a long ball and Chennaiyin won this game by 5-1, where Elano scored twice.
International career
In 2004 Khabra was included to play for the India U16 in Japan and he played for India U-16 against Iran, Malaysia and Kuwait. Then in 2006 he was included in the India U19 team to play for the country against China, Bangladesh and Myanmar in Myanmar. In 2011, he got his first call for the India. Khabra made a assist for Sushil Kumar to score the goal in a friendly game against Qatar in 2011.