Scab is the most damaging disease of pecan in the southeastern United States. Pecan trees can attain 44 m in height, so managing disease in the upper canopy is a problem. Fungicide is ordinarily applied using ground-based air-blast sprayers. Although mechanical hedge-pruning and topping of pecan is done for several reasons, improved management of scab is an important reason in the humid, wet Southeast. Resulting shoot growth on cut limbs of susceptible cultivars could lead to more severe scab. In three experiments over three years, we explored the effect of hedge-pruning trees to ∼12 to 14 m compared with non-hedge-pruned trees. All trees received fungicide treatments (air-blast sprays and ≤3 aerial applications). Hedge-pruning either had no effect, or increased or decreased scab severity only slightly on leaflets, immature, or mature fruit (a -9.95 to +14.63% difference in scab severity compared with the control). However, height in the canopy invariably had a large and significant effect on scab severity, and amounted to a 0.05 to 73.77% difference in severity between the lowest and highest sample in the canopy. Fruit weight depended on sample height, with fruit most often weighing less when collected at greater sample heights. A robust relationship between fruit weight and scab severity was found at the highest sample heights where scab was also most often severe (R2 = 0.21 to 0.67, P < 0.0001). Hedge-pruning and topping pecan tree canopies to manage tree size will enable better fungicide coverage, reducing risk of a scab epidemic as more of the canopy is assured efficacious fungicide spray coverage.