Several authors have shown that precise measurements of transit time variations of exoplanets can be sensitive to other planetary bodies, such as exo-moons. In addition, the transit timing variations of the exoplanets closest to their host stars can provide tests of tidal dissipation theory. These studies, however, have not considered the effect of the host star. There is a large body of observational evidence that eclipse times of binary stars can vary dramatically due to variations in the quadrupole moment of the stars driven by stellar activity. In this paper, we investigate and estimate the likely impact such variations have on the transit times of exoplanets. We find in several cases that such variations should be detectable. In particular, the estimated period changes for WASP-18b are of the same order as those expected for tidal dissipation, even for relatively low values of the tidal dissipation parameter. The transit time variations caused by the Applegate mechanism are also of the correct magnitude and occur on time-scales such that they may be confused with variations caused by light-travel time effects due to the presence of a Jupiter-like second planet. Finally, we suggest that transiting exoplanet systems may provide a clean route (compared to binaries) to constraining the type of dynamo operating in the host star.