Purpose In this work, we combine three-dimensional echo planar imaging (3D-EPI) with controlled aliasing to substantially increase temporal resolution in whole-brain functional MRI (fMRI) while minimizing geometry-factor (g-factor) losses. Theory and Methods The study was performed on a 7 Tesla scanner equipped with a 32-channel receive coil. The proposed 3D-EPI-CAIPI sequence was evaluated for: (i) image quality, compared with a conventionally undersampled parallel imaging acquisition; (ii) temporal resolution, the ability to sample and remove physiological signal fluctuations from the fMRI signal of interest and (iii) the ability to distinguish small changes in hemodynamic responses in an event-related fMRI experiment. Results Whole-brain fMRI data with a voxel size of 2 × 2 × 2 mm3 and temporal resolution of 371 ms could be acquired with acceptable image quality. Ten-fold parallel imaging accelerated 3D-EPI-CAIPI data were shown to lower the maximum g-factor losses up to 62% with respect to a 10-fold accelerated 3D-EPI dataset. FMRI with 400 ms temporal resolution allowed the detection of time-to-peak variations in functional responses due to multisensory facilitation in temporal, occipital and frontal cortices. Conclusion 3D-EPI-CAIPI allows increased temporal resolution that enables better characterization of physiological noise, thus improving sensitivity to signal changes of interest. Furthermore, subtle changes in hemodynamic response dynamics can be studied in shorter scan times by avoiding the need for jittering.