Goals in either half from Jonjoe Kenny and Dominic Calvert-Lewin gave the Toffees their victory.
After taking their time to get into the game, North End contested it well in the main and had their chances.
Ethan Walker, Jayden Stockley and Jordan Storey all forced good saves from home keeper Harry Tyrer, with Storey's header pushed against the bar.
Kenny gave the Premier League hosts a ninth-minute lead, an advantage doubled by Calvert-Lewin from close range in the 65th minute.
North End will have got plenty out of the game though, it being a good fitness work-out a week before the start of the Championship campaign.
Alex Neil had flipped the squad over for this game, naming a different starting XI to that at Sheffield United on Friday.
Academy product Walker was given a start, the 18-year-old playing on the right-wing in a front line which was led by Stockley with Josh Harrop on the left.
Brad Potts played the advanced midfield role, Paul Gallagher and Tom Bayliss deeper.
It was all Everton in the opening stages, with them dominating possession and forcing North End to chase the ball.
In the first minute, Gylfi Sigurdsson's shot caught a big deflection and Connor Ripley produced a fine reflex save to tip it over the bar.
The Toffees took a seventh minute lead, the defending for it not the greatest from a Preston perspective.
Richarlison's cross from the left was helped on by Theo Walcott in the box, right-back Kenny sliding in with two PNE defenders to knock the ball past Ripley.
In the ninth minute an angled shot from Richarlison was pushed away by Ripley diving to his left, then Bernard's shot from 20 yards whistled just wide of the post.
Gradually North End began to get a foothold in the game, seeing more of the ball and being able to start building attacks.
Paul Huntington glanced a header across goal and wide of the far post after climbing to meet Paul Gallagher's free-kick into the box
Just before the half-hour mark Harrop and Mason Holgate chased for possession in the Everton half, Harrop getting there just before the defender and knocking the ball to Potts who played Stockley clear.
The big striker didn't look too confident as he advanced into the box though, his shot too close to keeper Harry Tyrer who pushed it behind.
Kenny was shown a yellow card in the 37th minute for a high boot which caught Stockley in the chest, the resulting free-kick just outside the box curled just wide by Gallagher.
Just before half-time Walker raced down the right channel and cut into the box.
Coming in at an angle he had Harrop well placed in the middle but he chose to have a shot, the teenager's shot forcing a good save from Tyrer who gloved it behind.
It took a little while for either side to settle down in the second half before Everton had a decent spell.
Walcott put a header over the bar from Kyle John's cross, with Ripley having to save with his foot from Anthony Gordon's low shot.
At the other end, Bayliss had the ball in the hosts' net but the flag had gone up for offside against Harrop earlier in the move.
Everton doubled their advantage in the 65th minute, Bernard surging through midfield before playing the ball out to Richarlison on the left.
The Brazilian forward delivered a low cross into the middle which Calvert-Lewin slid in to knock against Ripley and into the net.
Neil made three substitutions in the 73rd minute, Joe Rafferty, Daniel Johnson and Adam O'Reilly replacing Darnell Fisher, Gallagher and Walker.
PNE were inches away from narrowing the deficit four minutes after that triple change, only for a combination of keeper Tyrer and the woodwork to deny them.
Harrop's free-kick from the right was met in the middle by Storey, the centre-back's close range header superbly pushed up on to the bar by Tyrer.
With two minutes left, Ripley made another good save to push out a powerful drive from sub Yannick Bolaise.
Everton: Tyrer (Hansen 90), Kenny, Holgate (John 31), Gibson, Nkounkou, Sigurdsson, Gordon (Baningime 78), Bernard (Adeniran 87), Walcott (Bolaise 67) Richarlison, Calvert-Lewin (Simms 82).
PNE: Ripley, Fisher (Rafferty 73), Huntington, Storey, Earl, Bayliss, Gallagher (Johnson 73), Walker (O'Reilly 73), Potts (Baxter 87), Harrop, Stockley. Subs (not used): Pearson, Bauer, Davies, Hughes, Ledson, Barkhuizen, Bodin, Hudson.
Referee: Robert Jones (Merseyside)