Whelan joined Aston Villa on 20 July 2017 on a two-year contract for a fee of £1 million. He scored his first goal for Aston Villa in a 4–2 win at Sheffield Wednesday on 24 February 2018. Whelan played 35 times in 2017–18 helping Villa reach the 2018 EFL Championship play-off final where they lost 1–0 to Fulham. He made 38 appearances in 2018–19 as Villa again managed to reach the play-off final this time beating Derby County 2–1. At the end of the campaign Whelan's contract was not renewed by Dean Smith.
