Bojan made his return in Sunday's Colonia Cup defeat against Portugese side FC Porto and played just over an hour.
Hughes said he was happy with the striker's progress, but insisted it would take time before the diminutive playmaker was back to his best.
"It was good to give him a decent run out because that's what he now needs," Hughes told the club's website (stokecityfc.com).
"It's obvious at the moment that he is not quite there yet and he understands that but with the progress he is making then he will get there very soon, but it's one of those things that will certainly take a bit of time," Hughes added.
Bojan was key to the exciting style of football Hughes got the Potters playing last season after taking the reins from fellow Welshman Tony Pulis.
The 24-year-old former Barcelona player scored crucial goals in wins over Tottenham, Arsenal and Everton before injury brought his season to a premature end.
"He is training every day with the rest of the group now, so we will continue to be patient with him and hopefully get him back sooner rather than later," Hughes said.
(Reporting By Simon Jennings in Bengaluru; editing by Sudipto Ganguly)
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