Since the process is long and involves more than one route to follow, I made this diagram to help:
The parts come apart in the order numbered above. Take note that there are two separate routes to get parts off -- taking the front off, and taking the rear off. It is noteworthy that this is the procedure I use to dismantle a PCX. You may be able to find shortcuts (for example, you can take the underseat bin out with the seat still attached without removing anything else but the rear wing, like I did in the suspension tutorial).
Start the procedure with a clean bike. It makes removing all the screws and bolts easier.
Flip the seat up and remove the two screws on the rear wing. It clips with one clip in the center of the back and two in the front. Pry up gently.
Unbolt the 4 bolts holding the rear wing support up.
Gently pry the rear wing support out from under the rear left and right fairings. Pull it out toward the back of the bike.
Remove the two bolts holding the seat on. Be careful that the nuts don't fall down into the scooter, you may want to keep a finger on them from the backside to support them.
Remove the fuel cover area. Two screws in front, and one big one towards the seat. It has little clips on the left and right side, so push it down and towards the seat. The flap itself binds on the battery box, so you have to flex it around some. Be gentle, you'll get it out.
Remove the rear left and right fairing / taillight assembly next. There's lot of screws and tabs, so don't force anything.
The first two screws are hidden down by the fuel cap.
Two more on either side of the seat mount.
Two more under the scooter, by the rear wheel.
Two bolts on the taillight.
Then, slide the whole assembly backwards. Don't pull up until the tabs are back.
A closeup of the tabs, so you don't break them.
Unplug the wiring harness before yanking the taillight off. Mine's a bit of a mess from adding aftermarket blinkers, but it should be fairly straightforward -- match color to color when reassembling.
Remove the battery box. There is a screw at the top, or a push clip depending on model. Push in the middle of the clip if it has no screw, and pull the tab at the bottom. If there is a screw, unscrew the screw at the top, then pull the tab at the bottom.
We'll remove the underseat bin next. There were two bolts hiding under the battery cover, remove them.
And unbolt the 4 bolts at the bottom of the underseat bin. Note that the black bolts are all up front, and the two silver ones go in back. Unclip the battery too.
Lift the bin out. There's the top of the engine! If you've got small hands, you can actually remove the engine at this point for installing big bore kits or whatever else. This is the point where you can do a valve adjustment easily as well.
We have most of the rear disassembled at this point. We'll remove the lower left and lower right fairings next -- note that the lower left and right fairings could have been removed at the start, without removing any panels from the rear end. Start by peeling back the rubber floorboards. They are just held in place by rubber grommets.
Remove the screws going down the outside edge. There are 5 per side. You can leave the screw on the spark plug cover for now (the one on the left side, for the small black access door)
Remove the sneaky little screw up front, in the wheel well.
Remove the silver bolt below the passenger footpeg on each side.
And the one by the kickstand.
Note that we did not need to remove the 3 silver bolts on each side where the floorboards are. Those bolts hold the floorboards in place, which require a lot more panels to come off to get to. I removed them in my pictures below, so just pretend they're there for now.
The floorboards are removed parallel to the ground, straight out to the left and right of the bike. Note the tab locations, and slide them out gently. You will have to put the kickstand down on the left side to remove the left panel.
We will disassemble the front end next.
Look up under the windscreen, there are two tiny little screws holding the front cover in place. You can hardly see them in this picture, but they're to the right and left side up in there on the white fairing. Undo them.
Gently pry off the front cover, there is a clip on the right and left side. The clips pry up and forward.
Remove the four nuts holding the windshield on, and remove the windshield.
Pry up the EVIL meter cover / dash cover panel that is under the windshield. This is a very difficult part to pry off, and my 2nd least favorite part of this disassembly process. I use plastic pry bars and do this on each side:
After one side is pried off, the other should be easy.
I should note that there is more than adequate room inside the dash here to put a horn. I put my Stebel Nautilus ear destroying horn in there, it's LOUD. I'll update that how-to later.
Next, we're going to remove the most evil part of the PCX, the clipped on inner cover. This is by far my least favorite part of disassembly, it's nearly impossible to pry off without breaking the part.
Open the glovebox, and get leverage. The clips are parallel to the ground, and they unclip straight towards the rear of the bike.
Removed. You can see the clips on the part here. Note how I broke the bottommost one off. Bah. It'll still be fine without it.
The cover around the keys pries off too, it just is slightly easier to pry off.
Get in there with a pry bar and start tugging.
Here's the clips:
Now to remove the inner fairing. Note the silver middle bolt and the two screws at the top left and right.
And the two screws on the bottom left and right.
And the two screws up at the top.
If you have the US model, peel the rubber boots for the blinkers back.
The panel has clips that run parallel to the bottom line of the fairing, so slide it downwards and backwards:
Now we can see the innards of the dash. There's a LOT left to remove.
Remove the four screws at the top left and right, front and back to remove the meter panel. I've circled them on the picture below.
Remove the two allen bolts holding the chrome cover around the handlebars in place, and remove the section closest to the front of the bike.
Go to the back of the meter panel, and gently peel back the rubber boot around the wiring harness. Unplug the wiring harness, it's just one big clip.
Lift the meter panel out. It has two large pins on the front that go into rubber grommets, so lift it towards the back of the bike and upwards.
Remove the left and right front fairings next. There are a TON of screws, so this will take you awhile.
Back on the picture from the meter cover, you can see a screw holding the headlight on below the meter screw. Remove that.
And remove the silver screw below it.
And the silver screw below that. It's way up in there, waaaaay back. Ignore the red and black wires there, your bike won't have those. They're from my 12v outlet.
Get the sneaky ones up in the wheel well, there are two per side.
And the ones that were under the rear left and right cover, near the fuel cap.
I didn't get pictures of it, but the fairing has tabs on the bottom of it. Slide each one towards the back of the bike until the tabs undo, then lift off.
Remove the screw holding the wheel well to the floorboards on each side.
The wheel well can just come out at that point.
Remove the silver bolts holding the floorboards in place, and remove them. Ignore the two white wires in the pic below, your PCX won't have them. They're for my aftermarket horn.
At this point, the PCX is completely naked, save the front and rear mudflaps. The front mudflap detaches with a bolt on each side, and I don't remember how the stock rear mudflap attaches (mine is aftermarket).
The naked PCX:
Reassemble in the reverse order, and reply if you have any questions on the process.

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