Applying foliar fungicide and raising cut height at harvest may increase the nutritive value of whole-plant corn silage (WPCS). The objective of this study was to evaluate the effects of foliar fungicide application (prothioconazole and trifloxystrobin; Delaro, Bayer CropScience) and harvest cut height on the fermentation profile of WPCS ensiled for 0, 30, 60 and 90 d post-harvest. Fungicide treatments were randomly assigned, and replicated 3 times, to one of 16 0.21-ha plots as follows: control (CON), plants received no application; (V5), plants received one application at corn vegetative stage 5 (V5); (V5R1), plants received 2 applications at V5 and corn reproductive stage 1 (R1); (R1), plants received one application at R1. WPCS was harvested on August 30, 2017 at 34.0 ± 1.6% dry matter (DM). Each plot consisted of 16 rows; 8 were harvested at 30.5 cm (LC) and 8 were harvested 56 cm (HC). From each plot, 3 mini-silos containing 600 g of composited WPCS were immediately vacuum-sealed (Minipack MVS-20, Doug Care Equipment, Springville, CA). Mini-silos at 0d were immediately frozen. Remaining mini-silos were allowed to ferment at room temperature before freezing at 30, 60, and 90d. A VFA score of 0–10, 10 being the most desirable, was used to evaluate overall silage quality (Diary One, Ithaca, NY). At 90 d, V5 had a higher (P = 0.02) VFA score than CON (9.66 and 9.42; SEM = 0.07, respectively). At 60 d, fungicide treated corn had higher (P = 0.03) lactic acid concentrations than CON corn (8.02%, 8.92%, 8.52%, 8.33%; SEM = 0.26 for CON, V5, V5R1, and R1, respectively). At 60 d, fungicide treated corn had higher (P = 0.0006) ammonia-N concentrations than CON corn (4.00%, 5.38%, 5.38%, 5.13%; SEM = 0.33 for CON, V5, V5R1, and R1, respectively). At 90 d, HC corn had less (P < 0.0001) lactic acid (9.49% and 8.15%; SEM = 0.17, respectively) and a lower (P = 0.0002) VFA score (9.59 and 9.25; SEM = 0.05, respectively). In conclusion, raising cut height did not improve fermentation. However, fungicide application did improve fermentation of WPCS and has the potential to increase milk production when fed to dairy cattle.