Marssonina blotch in apples and pear scab are diseases that may affect apple and pear production as well as related industries significantly. The range and scale of the economic influence of such outbreaks should be clarified to ensure the sustainable growth of these industries. This study evaluates the direct and indirect economic effects of outbreaks through a partial equilibrium approach and an input-output model; direct influences are measured on the basis of reduced production, and the estimated costs are 34,926 million Korean Won (mKRW) (US$ 29.79 million) and 11,767 mKRW (US$ 10.04 million) for apples and pears, respectively. The indirect effects are determined according to changes in the quantity of apples and pears supplied to the market; these effects can induce social welfare losses. These costs are estimated to be 305,065 mKRW (US$ 259.08 million) for apples infected with Marssonina blotch, which accounts for 186,628 mKRW (US$ 158.50 million) in producer surplus and 118,437 mKRW (US$ 100.58 million) in consumer surplus and 72,693 mKRW (US$ 61.74 million) for pears infected with scab, which accounts for 44,106 mKRW (US$ 37.46 million) in producer surplus and 28,587 mKRW (US$ 24.28 million) in consumer surplus. The findings from this study can be referenced by the Korean government in designing more effective control measures toward sustainable growth of related industry.