You can, and you also can't...
If you use Images-to-GIF and you paste a transparent image, and go to 'More Options', then 'Background color' and you leave it blank, the GIF will be temporarily transparent. You could theoretically paste several frames of the GIF to make a full transparent GIF.
However, it only stays transparent while the .gif format, which supports transparency, is used. After a period of time, Imgflip will convert the .gif file into a .mp4 file, which does not support transparency. Since Imgflip relies on .mp4 by default, then it won't show up as transparent.
A solution to this would be to not convert to .mp4, but I doubt this will be considered because of the inefficiencies of .gif. Another one would be to support .webp, which supports transparent GIF-like animations. However it's notoriously hard to integrate, so I doubt Imgflip will add multi-frame .webp support to the GIF Maker.
Here's a transparent GIF:
imgflip.com/gif/746886
If you right-click on the GIF, press 'Download .gif' and open it, then you can see that it's transparent.
