Sitton was appointed joint caretaker manager at Leyton Orient with Chris Turner in April 1994, following the departure of Peter Eustace, and helped the team avoid relegation from the Second Division by earning four points from their last two matches. The co-managership was Sitton's idea, as he did not know many of the first team players since he moved into coaching in Orient's youth setup, and knew that Turner had more knowledge about them. The duo were given the job permanently that summer after the board received positive feedback from the players, and continued throughout the difficult 1994–95 season in which Sitton had to work in six different roles within the club whilst on a youth coach salary. The squad size was cut in half and the club was on the verge of liquidation, with the PFA paying the players wages for several months whilst chairman Tony Wood tried to sell the club.

During this time, he became one of the few football managers to feature in a Channel 4 documentary, Orient: Club for a Fiver (sometimes known as Leyton Orient: Yours for a Fiver), made in 1995 by Open Media. The programme highlighted Sitton's well-known passionate language and managerial style, and featured a half-time team talk given by Sitton on 7 February 1995, after Orient had fallen 1–0 down in a league match at home to Blackpool. After sacking defender and fan favourite Terry Howard on camera in the dressing room, Sitton addressed two other players and offered to fight them, saying:

"You, you little cunt, when I tell you to do something, and you, you fucking big cunt, when I tell you to do something, do it. And if you come back at me, we'll have a fucking right sort-out in here. All right? And you can pair up if you like, and you can fucking pick someone else to help you, and you can bring your fucking dinner. 'Cos by the time I've finished with you, you'll fucking need it."[4]
Speaking about the event later, Sitton said, "Terry's an ex-teammate of mine who I like very, very much. He's good company when you go for a night out – but as a manager and a coach, he's not what I'm looking for. I may have lost a friend, but by tomorrow I would have recovered."[5]

Orient went on to lose the match 1–0, and after winning only one of the next 15 games, both Sitton and Turner were sacked two months later. Orient won just seven of 47 games under the pair. After the pair left, the side lost the following three games and finished bottom of the table.

New owner Barry Hearn had briefly considered retaining Sitton on a three-year contract, before hiring Pat Holland as Sitton and Turner's replacement.