As the squad headed out for their Premier League clash against Newcastle, club chairman Phil Gartside told Sky Sports that a deal had been agreed on a fortnight ago and was already in effect.
"Gary signed a new contract a couple of weeks ago and we haven't actually announced it yet," Gartside said.
"That is the truth of the matter. Gary and I get on very well together and I know the quality of the work that is going on behind the scenes and there is no question about anybody else coming in.
"He has got a good team behind him and they have worked hard this year.
"Over the last 12 months we have had a lot of changes, about 22 players have gone out, we have had 10 or 12 come in, and we have got into a real transition period and I think we are beginning to get to the end of that."
Despite speculation surrounding his future being rife with rumours that Owen Coyle was being drafted in as a replacement this summer, Megson insists the news is 'not a big deal".
"It's not a new contract," he said. "When I signed it last week that was the first time I've signed a contract here, so it's not something that's a big deal at all to be honest."
Megson joined Bolton in Oct 2007 with the team odds-on for relegation but he led them to safety and preserved their Premier League status.
He has previously managed Norwich City, Blackpool, Stockport County, Stoke City, West Bromwich Albion, Nottingham Forrest and Leicester City.