Agriculture is the world’s most important industry. According to the structure, Šumadija district is mainly composed of arable land and gardens, which make up 69%. The increased amount of COVID-19 waste generated from medical activities in rural areas needs to be properly handled due to its contagious, even lethal properties. The aim of this study is an analysis of two drivers through the generation of COVID-19 waste, Central and local treatment site, proposed transport routes, and total cost in Šumadija district. Results showed the economic costs of transportation increased 2.5 times compared to before and after the emergence of the COVID-19 pandemic. Also, the increase in health risk was correlated to the increase in the per capita cost of transportation along the transportation routes. Analyses of human health risks and detailed financial calculations gave a clear insight in infectious waste management possible influence on agriculture.