The 54-year-old's Melbourne home was raided by police in January, which had led to seven charges, including trafficking ice and ecstasy and possession of LSD and ecstasy, 7 News report.
He is expected to face the Melbourne Magistrates’ Court on Tuesday afternoon.
Thompson's former housemate, Thomas Windsor, is facing charges of trafficking commercial quantities of amphetamine and ice as well as trafficking ecstasy, 9 News reports.
Thompson played 202 games for AFL club Essendon, including winning three premierships.