Atkinson made his debut for St Kilda after being a first-round draft pick in the 1992 AFL Draft. In his debut match in Round 11 1993 he had 25 touches and earned an AFL Rising Star nomination, but was dropped after one more match despite being among the best once more. In a shock decision, he was delisted at the end of the season.
In an interesting turn on events he was selected in the 1998 AFL Draft by Adelaide after trading Chad Rintoul to West Coast for pick 80. At age 26, and out of AFL for several years, his SANFL form with the Sturt Football Club was enough to get him re-drafted. Hampered by groin injuries, he played only five games in 1999 before being delisted once again.
On 24 October 2000, Atkinson was awarded the Australian Sports Medal for being a recipient of the highest individual honour in South Australian Football.