Further to the above, it might also help us to know what the pop-up actually says. For example, does it appear to be a system message (e.g. a Windows error message or something like "please install the latest version of Adobe Flash Player"), does it try to tell you (even if falsely) that there's a virus on your computer or does it invite you to click on a link to go to a website?
Does the pop-up appear when you boot into Safe Mode? (To get into Safe Mode with Windows XP, Vista, 7 and 8 keep tapping F8 during the boot-up process until you see a screen with various boot options. Use the up and down keys to navigate to 'Safe Mode with networking' and hit 'Enter'. For Windows 10, see here:
https://www.digitalcitizen.life/4-ways-boot-safe-mode-windows-10 ). If you can get into Safe Mode without the pop-up appearing it should be possible to tackle the problem from there (either by running an anti-malware program or by using System Restore).