 On 20 September 2019, it was announced that Flanagan was allowed to return to the NRL but under strict conditions.It was reported that Flanagan was still unable to hold a head coaching role at any club until 2022 but was allowed to return as an assistant coach.On 27 November, 2019, it was announced that Flanagan had joined his junior club the St. George Illawarra Dragons as an assistant coach to Paul McGregor beginning in the 2020 NRL season.