We present the first detection of the photometric variability in a spectroscopically confirmed Y dwarf. The Infrared Array Camera on board the Spitzer Space Telescope was used to obtain time series photometry of WISE J140518. 39+ 553421.3 at 3.6 and 4.5 μm over a 24-hr period at two different epochs separated by 149 days. Variability is evident at 4.5 μm in the first epoch and at 3.6 and 4.5 μm in the second epoch, which suggests that the underlying cause or causes of this variability change on the timescales of months. The second-epoch [3.6] and [4.5] light curves are nearly sinusoidal in form, in phase, have periods of roughly 8.5 hr, and have semi-amplitudes of 3.5%. We find that a simple geometric spot model with a single bright spot reproduces these observations well. We also compare our measured semi-amplitudes of the second-epoch light curves to predictions of the static, one-dimensional, partly cloudy, and hot spot models of Morley and collaborators, and find that neither set of models can reproduce the observed [3.6] and [4.5] semi-amplitudes simultaneously. Therefore, more advanced two-dimensional or three-dimensional models that include time-dependent phenomena like vertical mixing, cloud formation, and thermal relaxation are sorely needed in order to properly interpret our observations.