Uniform and minuscule Ru particles confined in NaY zeolite (Ru@NaY) are prepared via a simple in situ synthesis technique. Transmission electron microscopy studies indicate that the Ru particles are encapsulated within the micropores of NaY zeolite and form a uniform size of 1.5–3.5 nm. Thanks to the effective confinement of Ru particles within the NaY zeolite, as well as the high concentration of B-5 sites and basic sites, the prepared Ru@NaY catalysts show excellent NH3 decomposition activity and highly efficient H2 formation. Notably, the 0.1Ru@NaY catalyst achieves a 92.7% NH3 conversion and a H2 formation rate of 690 mmol min−1·gRu−1 at 500 °C and GHSV = 9000 mLNH3·gcat−1·h−1 and shows outstanding stability throughout a 95-h lifetime test. The encapsulation synthesis of Ru clusters in zeolites endows the catalysts with exceptional catalytic activities and excellent stability, thus providing new prospects for the production of H2 from NH3 decomposition.