Harkins missed last weekend's win over Hearts and he returns for a game Dundee must win to have any chance of avoiding relegation - although their fate could be decided by St Mirren winning against Hearts.
Winger Nicky Riley misses out after failing in his appeal over his red card against Hearts last week, as he starts a two-match ban.
The Dark Blues are still without Stephen O'Donnell (knee) and Jamie McCluskey (Achilles).
Aberdeen boss Derek McInnes will make a decision on the fitness of captain Russell Anderson before naming his team to face Dundee on Sunday.
The central defender did not train on Friday after missing last weekend's 1-0 victory over Kilmarnock with a hamstring injury, but he will do some light training on Saturday.
Fellow defender Andrew Considine (broken leg) and midfielder Chris Clark (broken ankle) are both out for the rest of the season as the Dons ain to finish top of the lower section in the SPL.