The Republic of Ireland Under-21 skipper went off at half time at Plymouth on Saturday with a groin injury.
It is expected though that the current Owls captain will be fit to play as Paul Sturrock is set to name an unchanged side - if not Burton O'Brien should replace Whelan.
A win is important for Wednesday as they look to escape the lower reaches of the table and Sturrock is looking for two back-to-back victories - especially with fellow strugglers Brighton coming to S6 next Monday.