Purpose: Microbeam radiation therapy (MRT) is an experimental pre‐clinical technique using arrays of microscopically‐thin, low‐energy X‐ray radiation to treat radio‐resistant, deep‐seated tumors. All previous MRT experiments were performed using synchrotron radiation. We have developed a compact MRT small animal system using carbon nanotube (CNT) field emission x‐ray technology. Our purpose is to incorporate respiratory gating to the MRT system, minimizing motion blurring and increasing the peak‐to‐valley‐dose ratio (PVDR), which is important for normal tissue sparing. Methods: A prototype CNT MRT system was employed. The intrinsically divergent radiation is collimated into ∼300um microbeams using an external collimator. Parallel microbeam planes were delivered by translating the object perpendicular to the microbeam plane in a step‐and‐shoot fashion. The device generated an average entrance dose rate of 1Gy/minute. For respiratory‐gated irradiation, electron field emission from CNT cathodes was synchronized with the respiratory cycle of the mouse so x‐ray radiation is only extracted during the motionless phase of respiration.A phantom simulating mouse respiration used a servo motor pushing on a pressure sensor in a typical breathing pattern. A control program used the signal to trigger x‐ray irradiation during the motionless phase. Two experiments were run: a single line irradiation at 160 kVp delivering 0.9 Gy/min for 5 minutes, and three such lines of irradiation separated by 900um. Dose profiles were measured with EBT2 Gafchromic dosimetry films. Results: A single beam showed a FWTM increase from 638 to 1088um with un‐gated motion. With gating, the FWTM was 669um, similar to the motionless case.PVDR quantifies MRT effectiveness in the case of multiple lines. Motion reduces PVDR 50 percent; with gating PVDR is almost entirely recovered, 5.5 percent higher than without motion. Conclusion: Gated MRT largely eliminates microbeam broadening from physiological motion, maintaining high PVDR. The technique increases precision and will be tested during MRT treatments.