Walker opened the scoring with Joe Rodwell-Grant adding North End's second from the spot before Akile Raffie and a trialist levelled things for Fleetwood, the second coming in stoppage time in the second half.
Walker then netted an impressive solo effort to give PNE the win.
Steve Thompson and Paul Gallagher named a strong Lilywhites side, sending out their side in a 3-4-3. Matt Olosunde continued his return to full fitness, with Greg Cunningham, Liam Lindsay, Joe Rafferty and Matt Hudson the senior players involved.
Luton Town boss says best team didn't win after Championship defeat to Preston North End
PNE player ratings vs Luton Town as Ben Whiteman and Liam Lindsay steal the show in hard-fought win
Match Report: Luton Town 0-1 Preston North End - Brad Potts stunner gives North End first Championship win
Preston North End boss felt his side found a way after wonder goal sees them past Luton Town
John Smith's PNE Fans' Panel verdict: Sunshine all the way
The game started with neither side able to take control, nor create chances.
The first chance came 24 minutes into the contest, Jacob Holland-Wilkinson getting on the end of Matt Olosunde's cross from the right, poking the ball at goal and forcing a good save from close range from Luc Rees.
PNE were ahead just four minutes later, Rodwell-Grant getting in behind and challenging for the ball before getting to the touchline and cutting it back fro Ethan Walker around 10 yards out. Walker's low strike was saved but not held as the winger was on hand to follow up and open the scoring.
North End would double their lead nine minutes later as Adam O'Reilly looked to cross from the right corner of the 18-yard-box, it struck an outstretched arm of Akile Raffie and the referee pointed to the spot.
Rodwell-Grant was the man to take the responsibility and he confidently dispatched the spot kick into the right side as the goalkeeper went left.
Fleetwood's best chance of the first half came from a dead ball after 39 minutes, Raffie's free kick from the left sid eof the box bent over the wall but comfortable for Matt Hudson in the Lilywhites' net.
Just before the break the Cod Army defence were called into action again, three minutes from time, Greg Cunningham's cross from the left cleared away from a trialist as Walker and Holland-Wilkinson both threw themselves at the ball.
After the interval, the first highlight of the second period was the visitors finding the net. Max McMillen was felled on the edge of the PNE box and a trialist stepped up to fire the ball into the top corner 57 minutes in.
Town continued to look the better side as another trialist threatened the North End goal three minutes later, jumping above Hudson as the 'keeper attempted to claim the ball.
The visitors were in more control of the game compared to the first half, though they could not force enough chances.
There was concern for the Lilywhites as Lewis Leigh was helped off the pitch through injury, slowly making his way to the touchline after 78 minutes.
Raffie tested Hudson after 89 minutes, driving an effort low from a tight angle before he went one better eight minutes later.
Three minutes into stoppage time the Town no.8 on the day hit a clearance header back where it came from on the volley. His strike stayed low and was deflected on its way into the corner of the net.
That was not the end of the goals however as Ethan Walker made sure PNE were victorious. The winger picked the ball up around half way and carried it to the edge of the Fleetwood box before jinking in between two defender and stroking the ball into the far corner after 95 minutes.
PNE Starting XI: Hudson, Rafferty, Lindsay, Blanchard (Mfuni, 70'), Olosunde (Slater, 61'), Leigh, O'Reilly, Cunningham (Green, 61'), Holland-Wilkinson (Pemberton, 74'), Rodwell-Grant, Walker.
PNE subs not used: Lombard.
Fleetwood Starting XI: Rees, Jones, Trialist, Bird, Trialist, Edwards, Raffie, Boyle, Trialist, McMillen, Trialist.
Fleetwood Subs: Eastham, Thompson-Prempeh, Marsh, Johnson, King.
Referee: M Mitchell.
Thanks for reading. If you value what we do and are able to support us, a digital subscription is just £1 per month for the first two months. Try us today by clicking here.