McPharlin was recruited from East Fremantle in Western Australia to the Hawthorn Football Club after being taken at Pick 10 in the 1999 AFL Draft. He made his debut in 2000, kicking a goal with his first kick, but played just 12 total games in his first two seasons at Hawthorn. Felling home sick in Melbourne, McPharlin jumped at the chance of returning to Perth, and was subsequently traded to Fremantle following the 2001 season. McPharlin battled injury early on in his career, managing just over 50 games in his first five seasons.