He began 2013 by filling-in on the United States and German teams during the 2013 Hopman Cup as a replacement for injured John Isner and Tommy Haas. Kokkinakis competed in the qualifying competition of the 2013 Australian Open, losing to Steve Johnson 15–17 in the third set. Kokkinakis sustained a stress fracture in his back in the Australian Open boys' final which kept him out of competition until mid 2013. He then returned to competition playing Futures tournaments in the Czech Republic, Canada and the United States with the highlight being a quarterfinal of the Canada F5 event. In September and October, Kokkinakis competed in two Challenger events in the United States. The first was the 2013 Napa Valley Challenger where he qualified and reached the second round, going down to Bradley Klahn despite leading by a set. Then in the 2013 Sacramento Challenger he qualified and made the second round. He again lost despite leading by a set against Nick Kyrgios. As a result of this, his ranking increased to a career best of number 655. In October, Kokkinakis paired up with Benjamin Mitchell and won the Melbourne Challenger defeating Alex Bolt and Andrew Whittington in the final in straight sets. This increased his doubles ranking by 453 places, which put him up to a career high of number 505. He also reached the second round in the singles. He looked like he would cause a big upset after taking the first set against Matt Ebden before losing the next two sets. He finished his year at the 2013 Traralgon Challenger where he lost in the second round to James Duckworth in straight sets.