2016 began with rumours linking him to rival NRL clubs in Sydney, most notably the St George Illawarra Dragons. However, he put that in the back of his head to lead Melbourne to a great start to the season. On the 2 April, he scored 2 tries to secure an 18-14 victory over the Newcastle Knights. 15 days later, he kicked a field goal in the 5th minute of golden point to give the Storm a 19-18 victory over the Wests Tigers. The Storm won 5 of their opening 7 games.
On 26 June 2016, Cronk became only the fifth NRL player in history to record 200 wins (from 289 games) in a 29 to 20 win over the West Tigers.
On 24 September 2016, in Melbourne's grand final qualifier against the Canberra Raiders, Cronk became just the 25th NRL player to notch up 300 first grade games. In doing so, he is only the 11th player to do so with the one club.
At the annual Rugby League Dally M awards on 28 September 2016, Cooper Cronk was named the Dally M Player of the Year for a second time after winning his first in 2013. Cronk tied with North Queensland Cowboys prop Jason Taumalolo to win. Cronk was also crowned Dally M Halfback of the Year earning the honours for the fifth time in his careers. This was further complemented on 22 December 2016, when Cooper Cronk won the 2016 Rugby League World Golden Boot Award (Worlds best player). The award is decided by a panel of Rugby League experts including Darren Lockyer.