Khune started out as a
striker when he arrived for trials at Chiefs in 1999, but assumed the gloves by chance after he experienced chest problems during a junior game and found himself being reduced to a
ball boy. Diving for balls that had missed the target he caught the attention of youth coach
Terror Sephoa who converted him to a
goalkeeper. In 2004, he was promoted to the first team. After three years of waiting to get any game time, Khune finally got his opportunity in the early stages of the 2007–08 season after the departure of number one goalkeeper
Rowen Fernandez to German club
Arminia Bielefeld. With the experienced
Emile Baron often plagued by injuries, Khune was made number one by then Chiefs coach
Muhsin Ertugral. He made his PSL debut against
Jomo Cosmos on 25 August 2007. His first season in the top-flight was highly successful as several match-winning displays for his side earned him a host of individual awards with Chiefs having the best defensive record in the league conceding only 19 goals in 30 games. In his second season, he often struggled to regain the form and consistency of the previous season even though Chiefs managed to finish third in the standings and win the
MTN 8. During the 2009–10 season a finger injury sidelined Khune for three months giving understudy
Arthur Bartman a chance to play regularly in his absence. In October 2011, Khune was assigned as captain replacing
Jimmy Tau. The 2012–13 season was arguably his best with Khune leading his side to a league and cup double. He was also voted into Goal.com's Goal50 which is a list of the best players of 2013. He was ranked 45th ahead of
Fernandinho,
Robbie Keane, and
Frank Lampard and behind
Andrea Pirlo,
Roman Weidenfeller,
Victor Wanyama and
James Rodríguez who were all ranked from 40 to 50. He made his 200th appearance for Chiefs against
Mpumalanga Black Aces in 2014. Prior to that match he had 91 clean sheets in 199 games and at the beginning of the season, he had played 172 games for Chiefs. In the 2013–14 season he won the Goalkeeper of the Year award for the second time in a row with 15 goals conceded and 18 clean sheets in 25 starts beating
Moeneeb Josephs and
Anssi Jakkola. Around July 2014 he was linked to a move to
Bundesliga club
Hannover 96. On 3 September 2014, Khune was diagnosed with a Grade 3
stress fracture which he initially suffered from since February 2014. His injury cost him his place in the
2015 African Cup of Nations. He was declared fit to play on 23 February 2015 although he did suffer a minor injury after clashing
Morgan Gould's studs to his ribs which left a mark in a 4–0 win over Edu Sports in the
Nedbank Cup. On 9 April 2015 in a 1–0 win over AmaZulu, Khune was controversially sent off in the 82nd minute in a game which also produced nine yellow cards – after receiving two cautions in quick succession from referee Phillip Tinyane at Peter Mokaba Stadium. Khune was first booked for time-wasting before being given his marching orders for showing dissent at the decision. Khune took to
Twitter saying: "@OfficialPSL I did nothing wrong. You guys need to take action against these poor referees. "It's about time action is taken against these referees by @OfficialPSL. They've been very poor since beginning of the season. It's unfair how we are painted bad for our actions on the field but we are provoked by these referees, [you] can call me names but I stand for what is right." The league then afforded Khune five days to explain his comments although Khune did issue a public apology. Khune initially did not renew his contract with Kaizer Chiefs when it expired in June 2015, however, after a long period of negotiations, he returned to the club on 30 July 2015, signing a new contract. ==International career==