Pesticides in urban runoff are a major source of pollutants in aquatic ecosystems. Fipronil, a phenylpyrazole insecticide, found in structural pest control products, turf grass control, and home pet flea medication, has recently increased in use and is commonly detected in urban runoff. However, little is known about the effects of fipronil on aquatic organisms at early developmental stages. Here, we evaluated toxicity of fipronil to embryos of Japanese Medaka (Oryzias latipes, Qurt stain) using a high-throughput 96-well plate toxicity test. Male and female embryos (< 6 h post fertilization) were exposed to concentrations of fipronil ranging from 0.1–910 μg L−1 for 14 days or until hatching. Embryos were subjected to gross and microscopic examinations of developmental adverse effects as well as transcriptome analysis using RNA-seq. Results indicated a positive dose-response in reduced hatching success, increased gross deformity (tail curvature) at a lowest-observed-effect concentration (LOEC) of 200 μg L−1 and delayed hatching (~1 day at the highest concentration, LOEC = 600 μg L−1). The transcriptome analysis indicated that fipronil exposure enhanced expression of titin and telethonin, which are responsible for muscle development. It is therefore possible that the formation of a tail curvature is due to asymmetrical overgrowth of muscle. Our results indicate that sub-lethal effects occur in embryonic stages of an aquatic vertebrate following exposure to high concentrations of fipronil, although no adverse effects at the highest published environmentally relevant concentration (6.3 μg L−1) were observed.