Fipronil, a broad-spectrum insecticide, is widely used in agriculture and veterinary practices. Fipronil-induced neurotoxicity and potential adverse effects on humans and aquatic organisms have raised health concerns. Monitoring programs have been implemented globally to assess fipronil residues in food, including fruits, vegetables, and animal products. However, previous exposure assessments have often focused on specific food categories or subsets of items, resulting in limited insights into the overall health risks. Additionally, the large number of non-detect fipronil residues in food has introduced uncertainties in exposure assessment. To address these issues, a probabilistic exposure assessment and dose-response analysis were adopted in this study, considering the sample distribution below the detection limit to better characterize uncertainties and population variability in health risk assessments. The estimated fipronil exposure to the general public ranges from 6.38 × 10−6 ± 0.00017 mg/kg/day to 9.83 × 10−6 ± 0.00034 mg/kg/day. Only one out of 200,000 simulated individuals had a fipronil dose exceeding the probabilistic reference dose (0.048 mg/kg/day, pRfD), which aims to protect 99% of the population with effects less than 10% extra risk. By incorporating uncertainties in exposure and dose-response data, a more comprehensive understanding of the health risks associated with fipronil exposure in the Taiwanese population has been achieved.