I must begin with the first rule of loli-fying your uniform: Check Your School's Dress Code!
Some schools have a more relax dress code and that gives you ample opportunity to move around within the rules; while other schools have a very strict dress code and will be limited with what you can do.
Once you've reviewed you school's dress code and have an idea of your wiggle room, proceed.
Choose a skirt, even without a petticoat a skirt is more loli than a pair of pants (unless you're going for kodona)
Peter pan style collars are definitely an option, maybe you can look of something with pin-tucks and ruffles (if its allowed of course), this one from lands end is excellent for our purposes. Good news some lolita blouses can work with uniforms (again check your school's dress code before proceeding). Cutsew are also a great alternative, this version with Peter pan collar some even have a cute ruffle. Now isn't that Loli.
Sweaters and Coats:
Some schools are strict when it comes to outerwear, others are more relaxed, letting you wear any style. You might be able to sneak a brand sweater or coat (though I would be careful since sweaters and coats do have a tendency of disappearing or being forgotten). If your school only allows certain styles, then find one that is an accordance with the rules and still has a loli-able aspect.
When choosing shoes go for flats in mary-janes, ballet, or t-straps styles. Most school dress codes will allow flats over heels, still don't be tempted to take your Tea Party Shoes; they might not comply with the unstated rules... check with your school authorities beforehand.
Socks and stockings:
Another essential in the Lolita coordinate. Again resist temptation don't wear your Baby or AP brand socks. Opt for simple no frills solid white, black, grey, or brown knee socks or tights and match them to the color of your uniform.
We lolis love accessories, they make the outfit. For school though be as understated as possible. No head eating hair bows, or Decora methods of accessorizing. Your teacher might take anything too distracting from you and sometimes you won't ever get them back. Instead wear a simple Matilda-esque ribbon in your hair or a small bow diadem, choose just one ring, bracelet, brooch, etc that will show your personality but won't risk you getting in trouble.
Writing materials and Backpack:
Your most important school accessories. If your school's dress code doesn't give you any wiggle room then exploit the opportunities you do have. Your writing materials(pencils, notebook, bookcovers;)and your backpack (or purse, or messenger bag) are a great opportunity to express your taste and styles. Look for stationary, notebooks, backpacks, pencils, pens, etc that are loli-esque.
Most importantly please follow your school's dress code and rules. I know it can be tempting to take it OTT at school, but it isn't worth the risk of being reprimanded or having your items taken away. At some school breaking the dress code can have you wearing a large pink or neon orange t-shirt for the rest of the school day so know your school's rules before you decide to experiment.