The footman had an affair with the Duke of Crowborough (Charlie Cox) and tried it on with Turkish envoy Kemal Pamuk (Theo James) in the period drama's first series, but his homosexuality was not mentioned in the show's second run.
The 35-year-old quipped that he asked creator Julian Fellowes about the issue, and promised that Thomas's sexuality will be explored in the future, reports The Sun.
"The gay thing comes back in this series," James-Collier said. "He stopped being gay in series two!
"I had to ring upstairs and ask Julian, 'Am I still gay?' I said, 'Right, OK'.
"Seriously, in series two the drama focused on the Second World War and the huge impact it had on people back home in Britain in dealing with the dead and wounded. The gay thing was largely ignored.
"But Thomas has a beautiful storyline which evolves right through the new series and there is a massive pay-off."
The former Coronation Street actor went on to say that he had a number of "emotional" scenes to film in the new series, which he found "very challenging".
"I hope the audience will identify with why Thomas is the way he is - he has this secret which he can't tell anyone about because [homosexuality was] illegal," he added.
"He has this burden which he wants to share and we see that explained in a lovely storyline, thanks to Lord Fellowes."
Downton Abbey's third series will air in the autumn on ITV1 in the UK. It will air in the US on PBS on January 6, 2013.
> Rob James-Collier: 'Downton Abbey is the best job I've ever done'
> Rob James-Collier: 'Gay kiss is my idea'
Watch the cast of Downton Abbey discuss series three with Digital Spy below: