Croatia international Rakitic was dropped from the side for last Sunday's LaLiga trip to Villarreal amid reports he was the subject of interest from City.
Luis Enrique denied there was any truth to the claims following a 1-1 draw at the Estadio de la Ceramica, while vice-president Jordi Mestre said Barca were in the process of negotiating a contract renewal for the midfielder.
The rumours have rumbled on despite Barca's stance and Rakitic could be back in action for them Wednesday when they host Athletic in the second leg of their last-16 Copa tie, aiming to overturn a 2-1 deficit.
While Rakitic returns to the matchday squad, Portugal international Andre Gomes, who has failed to impress since his arrival from Valencia in July, has been left out.
Luis Enrique has Jasper Cillessen available once again, the Netherlands international having recovered sufficiently from a calf injury.
Jordi Masip, Aleix Vidal and Jeremy Mathieu have been left out of the matchday squad.