Farmers in developing countries are exposed to pesticide hazards due to unsafe handling. This study was conducted to identify the prevailing practices of pesticide use and factors affecting the handling of pesticides among the farmers of Chitwan, Nepal. A cross-sectional study was conducted among 125 farmers. None of the farmers completely followed all the protective measures. About 59% disposed the empty pesticide containers to a nearby water source and 62% preferred house ceilings as a storage place. Males (aOR = 3.99, CI = 1.63-9.78) and older farmers (aOR = 6.18, CI = 2.59-14.72) were more likely to smoke or chew tobacco during the process of spray. Males (aOR = 2.42, CI = 1.03-5.67), literate farmers (aOR = 3.56, CI = 1.51-8.33), and farmers aware of color coding (aOR = 2.67, CI = 1.13-5.67) were more likely to read the labels on pesticide bottles. In spite of an extensive use of pesticides, the farmers were not following proper and safe handling practices, exposing them and the community to a potential pesticide hazard.