Despite the use of best management practices for nitrogen (N) application rate and timing, significant losses of nitrate nitrogen (NO3(-)-N) in drainage discharge continue to occur from row crop cropping systems. Our objective was to determine whether a autumn-seeded winter rye (Secale cereale L.) cover crop following corn (Zea mays L.) would reduce NO3(-)-N losses through subsurface tile drainage in a corn-soybean [Glycine mar (L.) Merr.] cropping system in the northern Corn Belt (USA) in a moderately well-drained soil. Both phases of the corn-soybean rotation, with and without the winter rye cover crop following corn, were established in 1998 in a Normania clay loam (fine-loamy, mixed, mesic Aquic Haplustoll) soil at Lamberton, MN. Cover cropping did not affect subsequent soybean yield, but reduced drainage discharge, flow-weighted mean nitrate concentration (FWMNC), and NO3(-)-N loss relative to winter fallow, although the magnitude of the effect varied considerably with annual precipitation. Three-year average drainage discharge was lower with a winter rye cover crop than without (p = 0.06). Over three years, subsurface tile-drainage discharge was reduced 11% and NO3(-)-N loss was reduced 13% for a corn-soybean cropping system with a rye cover crop following corn than with no rye cover crop. We estimate that establishment of a winter rye cover crop after corn will be successful in one of four years in southwestern Minnesota. Cover cropping with rye has the potential to be an effective management tool for reducing NO3(-)-N loss from subsurface drainage discharge despite challenges to establishment and spring growth in the north-central USA.