The Republic of Ireland international had been out of action since early September because of a thigh problem.
However, he came through unscathed during his 63-minute run out against the Royals.
"I thought he did great," youth manager Alan Stubbs told the club's official website. "He's come through the game unscathed so that's a plus point and it's good for him that he's come through it and it's a step in the right direction for his recovery."
Gibson joined the Toffees from Manchester United in January of this year.