First, make sure you are using a theme that supports third-party addons like Fantastico. Some older themes and themes like x3mail do not support Fantastico.
You will need to check all of the following three things as any/all of these things may be the problem.
1) Make sure Fantastico is enabled, both in WHM's Feature Sets and that it is enabled in the WHM Fantastico admin settings.
2) Make sure you have a symlink to the Fantastico directory in every theme you use. For example if you use the "x3" theme:
ln -s /usr/local/cpanel/3rdparty/fantastico /usr/local/cpanel/base/frontend/x3
3) If you use the X3 theme, make sure your icon cache is up-to-date:
/usr/local/cpanel/bin/rebuild_sprites --force
If you get the following error after running rebuild_sprites:
Can't locate object method "newFromJpeg" via package "GD::Image" at /usr/local/cpanel/bin/rebuild_sprites line 17.
then you will need to install the Perl GD module first:
/scripts/realperlinstaller --force GD
After that, try rerunning the rebuild_sprites command above.
Please note that cPanel Inc. has discontinued support for the "x" and "x2" themes as of the release of cPanel v11. Although Fantastico does work in those themes we encourage you to switch to "x3" or another supported theme to ensure your users have the best experience possible.