The former Manchester United reserve team boss has agreed a three-and-a-half-year deal, but saw two goals conceded inside the first five minutes.
First, McCleary flicked in a through ball after 57 seconds and then drove home a right-footed shot from distance.
Yann Kermorgant's penalty sealed the Royals' third successive league win.
Wigan's fans were clearly not impressed after coming to see the dawning of a new era, soon booing after their dreadful opening.
Jaap Stam's side continued to have the better openings and Kermorgant might have had a brace himself had Jake Buxton not made two crucial blocks.
Joyce turned to his bench at half-time and Yanic Wildschut provided a spark, with Adam Le Fondre almost turning in his cross from the left, while another effort from the Latics forward had to be helped behind by former Wigan goalkeeper Ali Al Habsi.
But Kermorgant's goal, after Max Power tripped John Swift in the box, killed off the game as a contest and a further goal could have followed had Danny Williams kept his effort down when being set up by the impressive Swift.
A stoppage-time strike from Reading's Yakou Meite was also ruled out for offside as Wigan remained in the Championship's bottom three, while the visitors moved up to fourth.
Wigan manager Warren Joyce: "The first goal particularly, it's not like it's good play, it's just a straight long ball down the middle.
"It's the worst possible start you could get. The second goal was equally poor and then you've got a mountain to climb against a good side.
"You're under no illusions before the game starts that it's going to be a tough game, but we've given them a two-goal lead.
"It's basics even if you're in under-14 football - a straight ball goes down the middle after 90 seconds and they don't deal with it, two experienced players, you're 1-0 down and you've got a mountain to climb."
Reading manager Jaap Stam: "We spoke about what we can expect, with a new manager in, how they want to play, probably press us high up and don't give us time to play out from the back.
"The pace that we have up front we knew we could be a threat in behind if we do it well, if the runs are at the right time and we started doing that immediately and scored two early goals.
"You want to make it easy for yourself. After that sometimes we got a bit sloppy in how we wanted to play. You don't want to give goals away because it gives them confidence.
"How we played, how we defended, how we created chances, we did that very well and we deserved that win."
Match ends, Wigan Athletic 0, Reading 3.
Second Half ends, Wigan Athletic 0, Reading 3.
Offside, Reading. Chris Gunter tries a through ball, but Yakou Meite is caught offside.
Foul by Joey van den Berg (Reading).
Stephen Warnock (Wigan Athletic) wins a free kick in the attacking half.
Attempt blocked. William Grigg (Wigan Athletic) right footed shot from the centre of the box is blocked. Assisted by Yanic Wildschut.
Joey van den Berg (Reading) wins a free kick on the left wing.
Foul by Dan Burn (Wigan Athletic).
Attempt missed. Yanic Wildschut (Wigan Athletic) right footed shot from outside the box is close, but misses to the right. Assisted by Stephen Warnock.
Attempt blocked. Dominic Samuel (Reading) right footed shot from outside the box is blocked. Assisted by Yann Kermorgant.
Attempt saved. Yakou Meite (Reading) left footed shot from the right side of the box is saved in the bottom right corner.
Substitution, Reading. Yakou Meite replaces Garath McCleary.
Corner,  Reading. Conceded by Adam Bogdan.
Attempt missed. Michael Jacobs (Wigan Athletic) right footed shot from outside the box misses to the left. Assisted by Stephen Warnock.
Max Power (Wigan Athletic) wins a free kick on the right wing.
Foul by George Evans (Reading).
Substitution, Reading. Dominic Samuel replaces Callum Harriott.
Substitution, Reading. Joey van den Berg replaces John Swift.
Attempt blocked. Shaun MacDonald (Wigan Athletic) right footed shot from outside the box is blocked. Assisted by Yanic Wildschut.
Attempt blocked. Yanic Wildschut (Wigan Athletic) right footed shot from outside the box is blocked. Assisted by Nathan Byrne with a cross.
Corner,  Wigan Athletic. Conceded by John Swift.
Attempt blocked. Max Power (Wigan Athletic) right footed shot from the right side of the box is blocked.
Tyler Blackett (Reading) is shown the yellow card.
Shaun MacDonald (Wigan Athletic) wins a free kick in the attacking half.
Foul by Tyler Blackett (Reading).
Corner,  Wigan Athletic. Conceded by Liam Moore.
Attempt missed. Shaun MacDonald (Wigan Athletic) left footed shot from outside the box is close, but misses to the left.
Attempt blocked. Max Power (Wigan Athletic) right footed shot from the centre of the box is blocked. Assisted by William Grigg.
Substitution, Wigan Athletic. William Grigg replaces Adam Le Fondre.
David Perkins (Wigan Athletic) is shown the yellow card for a bad foul.
Callum Harriott (Reading) wins a free kick in the defensive half.
Foul by David Perkins (Wigan Athletic).
Corner,  Wigan Athletic. Conceded by George Evans.
Foul by Callum Harriott (Reading).
Nathan Byrne (Wigan Athletic) wins a free kick on the right wing.
Foul by Yann Kermorgant (Reading).
Reece Burke (Wigan Athletic) wins a free kick in the defensive half.
Attempt missed. Danny Williams (Reading) right footed shot from the centre of the box is high and wide to the left. Assisted by John Swift.
Goal!  Wigan Athletic 0, Reading 3. Yann Kermorgant (Reading) converts the penalty with a right footed shot to the bottom left corner.
Max Power (Wigan Athletic) is shown the yellow card.
Garath McCleary struck an early double as Reading thumped Wigan to hand Warren Joyce a nightmare start as the new Latics manager.