Rooney injured a toe in his left foot during United's first leg draw against Bayern Munich and he struggled in the return leg the following week.
The striker will travel to Goodison Park on Sunday though after making encouraging progress in his rehabilitation from the injury.
"Wayne Rooney has trained great this week," Moyes said.
"He is in really good form. Getting him back is a good thing.
"He just wasn't right with his toe at times in the last game."
When asked whether Rooney would be in the squad for the Everton match, Moyes replied: "Yes."
Moyes was in a good mood ahead of his first match back at Goodison Park since leaving the club to join United last summer.
His spirits have been lifted by the news that Robin van Persie is making a good progress in his return from a knee injury he sustained against Olympiacos.
Van Persie jarred his knee in the 3-0 win against the Greeks on March 21 and he has been sent to Holland to aid his recovery.
"Robin is making improvements," the Scot said. "We always thought he would be out for 4-6 weeks.
"We'll have a better assessment in the next week or so as we'll see how he is coming along.
"Our medical team is heading out there to see him this week and get a better feel as to exactly where he is."
Moyes confirmed that Marouane Fellaini has overcome a calf injury and should be fit to face his old club.
"Felli (Fellaini) didn't play against Bayern but we expect him back fit because he has trained all week," Moyes said.
Moyes ruled Rafael out due to a thigh problem while Jonny Evans is a doubt because of a long-term calf injury.
Sunday's fixture will be the first time Moyes has gone back to the club where he spent 11 successful years.
Moyes had tears in his eyes as he said his goodbyes to the Everton fans last May, but some Toffees supporters turned against him shortly after his departure.
A failed £28million bid from United for Fellaini and England left-back Leighton Baines angered some Everton fans and the Merseyside club branded the offer as "derisory" and "insulting".
That anger was evident when Everton supporters barracked Moyes during the Toffees' 1-0 win at Old Trafford in December.
Moyes was reluctant to speak about what kind of reception he might get at Goodison this weekend.
"The game is not about me, it's about Everton and Manchester United," he said.
"I was proud to be manager of Everton at that time but my job now is to make sure I get a result for Manchester United.
"The fans were always terrific in my time there, they were very supportive and always right behind the team.
"We had some really big games there at times and they'll be supporting the team like the Manchester United supporters have for their team."
Some had expected Everton to go through a year of transition under Roberto Martinez, but Moyes' successor has enjoyed a superb first year on Merseyside.
Everton are one point adrift of the top four and had it not been for a midweek defeat to Crystal Palace, Martinez's team would have been in pole position to pip Arsenal to the final Champions League qualification place.
Moyes, on the other hand, has struggled during his first term at Old Trafford.
Moyes admits it is almost "mathematically impossible" to catch Everton or Arsenal, but he does not begrudge his old side any success.
"I'm looking forward to going back as I had some great times and worked with great people and, more importantly, some great players," Moyes added.
"They were terrific and I'm really pleased to see them doing well.
"Roberto has done a brilliant job there in the time he has been in charge.
"He's got them playing well and in a good, healthy league position so I go back with some great feelings but I'm back now as Manchester United manager and my focus is on that now."
With United so far off the Champions League places, it is clear that Moyes needs to overhaul his squad if he is to challenge for a top-four finish next year, let alone the Premier League title.
The Scot has been linked with moves for Toni Kroos, Luke Shaw and a number of players from the Portuguese league, including William Carvalho, Eliaquim Mangala and Jackson Martinez.
Moyes says his attempts to bring in new players next year are progressing well, even though United are no longer able to offer Champions League football.
"I'm well into my planning with my thoughts and ideas getting ready for next year," he said. "We're linked with player after player and, every time I go to a game, I'm supposed to signing three or four players from that game.
"That isn't the case, but everyone is well aware we are looking to make signings and will try to do that whenever the opportunity arises.
"It will probably be after the end of the season before anything takes place but we have got to look to do one or two things."