It never pays to take shortcuts with your bathroom renovation. Even if there's already a toilet in place when you start a tile floor project, it has to come out; if not, the surface of the new tile will be higher than the toilet base, making it harder for you to notice potential leaks from beneath the fixture. Installing the toilet can only happen once your bathroom floor tiles, whether ceramic or vinyl, are properly installed. Depending on what kind of tile and adhesive you used, your waiting period may be anywhere from minutes to several days.
It's generally safest to wait 48 to 72 hours after installing ceramic tiles before installing the toilet.
Using Ceramic Tiles
Ceramic tiles give a bathroom a classic look. They're sturdy too, so hopefully your ceramic tile floors will last for years after they're installed. But the grout used between the tiles must be allowed to completely dry or it will shift when weight is applied to the floor. (Be sure to smooth down the grout lines so they are slightly below the surface of the tiles, and clean up all the excess grout from the tile surface.)
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After you lay ceramic floor tiles, the grout inside the joints between the individual tiles must be allowed to cure. Generally, it's safest to wait at least 48 but ideally 72 hours after installing ceramic tiles before installing a toilet. Pay attention to the manufacturer's instructions for the specific type of grout you've chosen.
Using Vinyl Tiles
Generally, the last step in installing vinyl tile is using a heavy roller to make sure that all the excess glue and air bubbles are removed from the tile, and that it is fully set. (You can rent such a roller from a home improvement store.) After that, the adhesive that is used to glue vinyl tiles to the floor must be allowed to fully dry before setting the toilet or any other objects on the tile.
There's a lot of variation in manufacturer's directions for vinyl tile, so how long it takes for your adhesive to fully dry depends on the kind of adhesive you've used. Follow the particular adhesive manufacturer's instructions for how long to allow the adhesive to dry. There are some kinds of spray adhesive that allow vinyl flooring to be used immediately after it's installed. With other kinds of adhesives, you may need to wait 48 hours or more before it's safe to install a toilet.
Also, if you use grout after installing vinyl tiles, the grout may require additional drying time before further work can be done in the bathroom.
While the Toilet Is Removed
While the toilet is off the flange, examine the flange's condition to make sure it's not broken. Also examine the floor area around the flange. This prevents you from installing new flooring over damage that should be repaired first. Cut the tile so it curves around the flange.
Toilet Installation Reminders
Be sure to scrape all the wax residue from the flange and from the bottom of the toilet, using a putty knife. Before installing the toilet, press a new wax ring onto the bottom of the toilet, or place the wax ring on top of the flange. With the additional height added by the tile, especially the thicker ceramic tiles, install extenders, if needed. Extenders are basically rings that raise the flange's height to be even with the new flooring so an effective seal can be created between the toilet and flange.