Diets fed to lactating dairy cows can contain 50% or more of whole-plant corn silage (WPCS). Fungicide can be applied to help minimize disease incidence. With decreasing agronomic prices, producers may try to reduce cost by not applying fungicide. The purpose of this experiment was to determine the effects of foliar fungicide application on floury and brown midrib (BMR) varieties of corn for WPCS on nitrogen utilization of lactating dairy cows. A 4 × 4 Latin square design balanced to measure carryover effects was used with 32 lactating, Holstein cows [BW = 649 ± 74 kg; DIM = 189 ± 49 d]. Treatments were floury WPCS with fungicide application (FF), floury WPCS with no fungicide application (FC), BMR WPCS with fungicide application (BF), and BMR WPCS with no fungicide application (BC). Fungicide (pyraclostrobin, C₁₉H₁₈ClN₃O₄ + metconazole, C₁₇H₂₂ClN₃O; Headline AMP, BASF, Florham Park, NJ) was applied at vegetative tassel (VT). WPCS was inoculated (Silo-King; Agri-King, Fulton, IL) and ensiled for 295 d before feeding. Statistical analysis was performed using the MIXED procedure of SAS (SAS Institute Inc., Cary, NC). Nitrogen intake was greater for cows in non-fungicide treatments (635.76 ± 15.3 g/d) than for cows in fungicide treatments (591.86 ± 15.3 g/d; P < 0.01). Milk protein nitrogen was greater for cows in non-fungicide treatments (159.83 ± 3.62 g/d) than for cows in fungicide treatments (143.98 ± 3.62 g/d; P < 0.01). Urinary urea nitrogen was greater for cows in non-fungicide treatments (236.33 ± 5.46 g/d) than for cows in fungicide treatments (209.68 ± 5.46 g/d; P < 0.01). Cows in FF excreted less nitrogen in manure (3.68 ± 0.15 g/d) than cows in FC (4.10 ± 0.15 g/d; P = 0.01). In conclusion, cows in fungicide treatments (FF, BF) excreted less nitrogen than did cows in non-fungicide treatments (FC, BC); however, cows in fungicide treatments also consumed less nitrogen.