A small rover, Noonan played in Fitzroy's inaugural VFL season in 1897 and then their inaugural premiership side the following year. In 1901 he crossed to Carlton and spent two seasons with the Blues.
Noonan spent the rest of his career in the VFA where he captained North Melbourne to premierships in 1903 and 1904. The rover also spent some time playing at Williamstown. He was the coach of North's VFL side in 1929 but couldn't spot them from finishing in last position, his only win coming in a game against Footscray.