If you mean using the Pathfinder Compatibility License, the following clause (from section 4: Usage Restrictions) prevents use in anything other than book, ebook or (free to use) website format:
"The license granted hereunder is expressly limited to use of the Compatibility Logo in printed books, electronic books, and freely available websites. Anyone seeking a license for any other use should contact Paizo directly, at licensing@paizo.com."
(I can see a possible workaround here, one I briefly considered using myself, which is to create the VTT as a free-to-use website monetized by ad revenue/donations)
You can do a virtual tabletop under the OGL* - which means not being able to use any Paizo trademarks such as "Pathfinder", even to indicate compatibility.
If you really want to reference "Pathfinder" in your product, you'll need to contact Paizo and work out licensing terms.
Alternatively, you might be able to use the Community Use License if you're willing to give the product away at zero charge and for non-commercial reasons (which likely means putting it on a non-commercial website for download, too, so you're probably unable to use it to promote other products or to gain ad revenue ;) )
* - But note you still have to meet the terms of the OGL, such as providing any open game content you use available within your software distribution in a human-readable form, which I believe can be done by ensuring you include text file versions of any OGC used. If you base it purely off the d20 SRD, you could likely meet the requirements by simply including a copy of the SRD itself on the disc/in the downloadable zip. If you use the Pathfinder PRD, the job will be a little more difficult as I believe you'll need to ensure you've removed any Product Identity references rather than a straight copypasta job.