Kilcoyne started Munster's opening pool game of the 2015–16 European Rugby Champions Cup against Benetton on 14 November 2015. On 19 February 2016, Kilcoyne scored two tries in Munster's 27–24 defeat against Glasgow Warriors in the 2015–16 Pro12. On 7 May 2016, Kilcoyne earned his 100th cap for Munster in their 31–15 win against Scarlets. On 4 November 2016, Kilcoyne scored two tries and won the Man-of-the-Match award in Munster's 33–0 win against Ospreys. On 24 January 2017, it was announced that Kilcoyne had signed a contract extension with Munster. On 5 May 2017, Kilcoyne was named in the 2016–17 Pro12 Dream Team. On 9 September 2017, Kilcoyne made his 100th appearance in the United Rugby Championship when he came off the bench against South African side Cheetahs in round 2 of the 2017–18 Pro14. Kilcoyne was Man-of-the-Match in Munster's 14–7 win against Racing 92 in Round 2 of the 2017–18 European Rugby Champions Cup on 21 October 2017.