I'm using Emacs 24 and elpy to run some Python 3 code. However, after I open a shell with C-U-C-C-C-Z and then run my code with C-U-C-C-C-C, I get the error in my command line: 

Cannot open load file: no such file or directory, pylint

This is odd, as I've made no recent changes to Emacs, but it always tends to be finicky about if it wants to run any code. The python shell works fine, so that shouldn't be the issue. Thanks.
Do you mean that it used to work ? To me this error means that the elisp pylint package was not installed or not "required". Try installing it with M-x package-install (and be sure to have the pypi pylint package installed in the current virtual env too, if you use one inside emacs -this is a current elpy installation shortcoming).
(made an answer of my comment)
Emacs fails to run Python code