Strikes from Godswill Ekpolo and Baily Cargill, either side of half time, put the Cod Army in a commanding position before a Wes Burns rocket made sure of the result at Highbury Stadium.
The Foxes, without international quartet Daniel Iversen, Alex Pascanu, Darnell Johnson and George Thomas, fielded a youthful side with four Academy scholars on the bench.
The first chance fell to the hosts as George Glendon floated a cross onto the head of Ashley Eastham after eight minutes but Max Bramley was able to watch it fly wide of his far post.
Nathan Pond found space in the 22nd minute to attempt a half-volley but shot-stopper Bramley, deputising for Iversen, did brilliantly to acrobatically tip it over his crossbar.
The Cod Army’s pressure eventually paid off four minutes later as a flowing move saw the ball fall perfectly for Ekpolo to place it beyond Bramley and into the corner from 16 yards.
Just before the break, Burns forced Bramley into another smart save with a speculative effort from the edge of City’s area but the visitors went into the break just a goal down.
Steve Beaglehole made a double substitution at the interval with forward Admiral Muskwe and young wing back Simran Thandi entering the fray for the second half.
Within seconds of the referee’s whistle, the hosts nearly doubled their advantage as Ashley Hunter went for goal from 20 yards. Luckily for the hosts, it struck the post and bobbled wide.
Uwe Rösler’s men, fifth in Sky Bet League 1, did get their second on the hour-mark as Cargill sprung to life in the box to nod Glendon’s smart free-kick into the back of the net.
With just five minutes remaining, Burns galloped down the right flank and powered it past Bramley from a tight angle to ensure that is was Fleetwood who secured all three points.
City were beginning to threaten on the break at Highbury Stadium just as Cargill pounced to double Fleetwood’s lead and take the match beyond Beaglehole’s men.
It was a moment which gave the hosts a cushion which they used all of their Football League experience to exploit, forcing the Foxes to push forwards.
Despite the result ultimately going against City in Lancashire, defender Sam Hughes impressed on his competitive debut for the Club’s Development Squad after an ankle ligaments injury.
Hughes, signed from National League side Chester this summer, had previously been forced to watch on as his colleagues enjoyed promising results against Everton and Manchester City in PL2.
Where does it leave us?
Beaglehole Disappointed With Defeat
Steve Beaglehole spoke to LCFC TV after his side's Checkatrade Trophy fixture against Fleetwood Town on Tuesday evening.
After the opening match, Leicester sit bottom of Northern Group A, with Fleetwood top, after Carlisle United overcame Morecambe 2-0 in the other fixture at the Globe Arena.
A 13-day break now awaits City before West Ham United visit King Power Stadium in PL 2 on Monday 11 September (7pm kick-off), which you can watch live on LCFC TV.
Leicester’s next outing in the Checkatrade Trophy, meanwhile, falls on Tuesday 3 October against Sky Bet League 2 outfit Carlisle at Brunton Park (7:45pm KO).
Fleetwood: Neal, Bell (Maguire 45), Eastham, Pond (c), Hiwula (Sowerby 76), Burns, Glendon, Ekpolo, Hunter (Grant 83), Schwabl, Cargill.
Subs not used: Cairns, Rodgers, Nadesan, Biggins.
Goals: Ekpolo 26, Cargill 60, Burns 85.
City: Bramley, Knight, Gordon, Ndukwu (Thandi 45), Choudhury (c), Hughes, Martis (Eppiah 62), Debayo, Wood, Watts, Kaba Sherif (Muskwe 45).
Subs not used: Yates, Shade, Leshabela, Ughelumba.
Referee: M Coy
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