Thyroid hormones are critically involved in somatic growth, development and metamorphosis of vertebrates. The structural similarity between thyroid hormones and triclosan, an antimicrobial compound widely employed in consumer personal care products, suggests triclosan can have adverse effects on the thyroid system. The sheepshead minnow, Cyprinodon variegatus, is now used in ecotoxicological studies that have recently begun to focus on potential disruption of the thyroid axis by endocrine disrupting compounds. Here, we investigate the in vivo effects of exposure to triclosan (20, 50, and 100 μg L−1) on the thyroid system and the embryonic and larval development of C. variegatus. Triclosan exposure did not affect hatching success, but delayed hatching time by 6–13 h compared to control embryos. Triclosan exposure affected the ontogenetic variations of whole body thyroid hormone concentrations during the larval phase. The T3 peak around 12–15 dph, described to be indicative for the metamorphosis climax in C. variegatus, was absent in triclosan-exposed larvae. Triclosan exposure did not produce any deformity or allometric repatterning, but a delayed development of 18–32 h was observed. We conclude that the triclosan-induced disruption of the thyroid system delays in vivo the start of metamorphosis in our experimental model. We observed a global developmental delay of 24–45 h, equivalent to 4–7% prolongation of the developmental time in C. variegatus. The costs of delayed metamorphosis can lead to reduction of juvenile fitness and could be a determining factor in the outcome of competitive interactions.