Emerging studies provide promising evidence that applying zeolite combined with water-saving irrigation could effectively retain soil nutrients and increase rice yields. However, the effects of this water-nitrogen management strategy on soil nitrogen (N) loss through leaching and runoff are unclear under field conditions. Herein, we explored the dynamics of N concentrations, quantified soil N losses through leachate and runoff, and investigated the response of reducing N loss on rice yield. A three-year field experiment (2018−2020) was conducted in Donggang city of Liaoning Province in northeast China. The field experiment used a split-plot design, including two irrigation regimes [continuously flooded irrigation (CF) and alternate wetting and drying irrigation (AWD)] as main plots, and two zeolite applications (Z0, no zeolite; Z10, 10 t ha−1 zeolite) as sub-plots, so as to quantify their effects on TN, NH4+-N, NO3−-N loss, and rice yield. Averaged across 3 years, our results showed that AWD reduced the volume of irrigation, leachate, and runoff by 22.2%, 20.8%, and 18.9%, respectively, compared with CF. AWD also decreased the losses of total N (TN), NH4+-N, and NO3−-N by 25.5%, 17.5%, and 11.1% in leachate and by 22.9%, 18.3%, and 26.3% in runoff, respectively, compared with CF. Compared to Z0, Z10 reduced the losses of TN, NH4+-N, and NO3−-N by 16.0%, 16.9%, and 19.4% in leachate and by 10.0%, 14.0%, and 5.9% in runoff, respectively. N output through leaching and runoff under AWD and Z10 was decreased by 2.1% and 2.2%, respectively, compared with CF and Z0. No significant difference was found in rice yield between CF and AWD, whereas rice yields increased 3.3% under Z10 compared with Z0. Altogether, our results highlight that the combination of zeolite and AWD can simultaneously produce more rice yield and reduce soil N losses.