A computer-implemented method for detecting illegitimate applications may include 1) identifying an installation of an application on a computing system, 2) determining, in response to identifying the installation of the application, that at least one system file with privileged access on the computing system has changed prior to the installation of the application, 3) determining that the application is illegitimate based at least in part on a time of the installation of the application relative to a time of a change to the system file, and 4) performing a remediation action on the application in response to determining that the application is illegitimate. Various other methods, systems, and computer-readable media are also disclosed.