Martyn was drafted to the Kangaroos under the father-son rule. He notched up his first league game against Geelong but did not come on until the third quarter where he lined up on Gary Ablett, Sr. In 2002 he made history by being the first man to ever play against father and son by playing against Geelong's Gary Ablett, Jr. (although Bruce Doull had played with both Silvagni's at Carlton). In 1995 he was awarded the Michael Tuck Medal after the Kangaroos beat the Adelaide Crows in the 1995 Ansett Cup. In 2002 he gained permission by the AFL to wear his father's number 30 jumper, as it would be the last match his father ever witnessed before dying a few days later. Martyn won two premierships with the Kangaroos in 1996 and 1999 until he was delisted by the Kangaroos at the end of the 2002 season. In 2000 after Matthew Lloyd kicked his 100th goal for the season in the first week of the finals, a big chested man ran threw him on the way to giving Lloydy a high 5 for kicking his 100th goal, this punctured Mick Martyn's left lung.
Martyn was injured in the 2002 Bali bombings where he received burns to the back of his scalp. He had been drinking with Jason McCartney at Paddy's bar at the time of the attack. After exiting the building, he and McCartney left the scene and were admitted to hospital, McCartney suffering more life-threatening injuries.
At the 2002 draft, with Denis Pagan needing a "gorilla" at full-back, Martyn was drafted by Carlton to play for the 2003 season. He played a handful of games to notch up his 300th match against Essendon in round 18 2003 at the MCG where Carlton lost by 34 points; after the match he was chaired off the ground. However, that turned out to be his last match; he announced his retirement after the serious injury he suffered the next week at training. He did cause some controversy during the year, commenting on radio that after the Bali Bombings "it wasn't the blue and white in my corner, it was the navy blue".