The Irish international looked likely to join Hull City on transfer deadline day in September after the Baggies accepted a bid for the striker.
However, the deal was pulled at the last minute, with both clubs blaming each other for the collapse.
The 26-year-old frontman has scored four goals in his last four matches for club and country, leading Clarke to question why he would ever consider cashing in.
"If Shane continues to play at the level he is right now the contract issue will sort itself out," Clarke told reporters.
"If he's on that level there's no doubt - but are you asking me if I'm selling Shane in January? No, I'm not.
"Why would I sell my best, most in-form striker? I don't think Shane will be going anywhere in January. I haven't considered it."
The former Reading player arrived at The Hawthorns for £6.5m in August 2011.