We present endoscopic focal modulation microscopy (FMM) for minimally invasive imaging of deep tissue with high contrast, and then compare the results using endoscopic confocal microscopy (CM). Deep tissue imaging is achieved using a needle-like endoscopic probe based on gradient-index (GRIN) lenses. A tissue-like phantom with fluorescent micro-beads and rat kidney tubules were imaged through the endoscopic probe with FMM. FMM effectively rejected the background signals from the out-of-focus plane, thereby enhancing the image contrast and the optical sectioning ability. The combination of the GRIN endoscopic probe and FMM provides deep tissue imaging with better contrast than endoscopic CM.