We investigated the prevalence of clinical trachoma in 154,265 children aged 6 to 16 years in 206 Shanghai migrant schools. Clean water availability in school, each child's facial cleanliness, eyelids, corneas, and the presenting distance visual acuities were examined. Trachoma was clinically diagnosed in accordance with the World Health Organization simplified classification. Eyes diagnosed with trachoma were swabbed to test for ocular Chlamydia trachomatis infections (OCTI) with a rapid latex immunochromatographic test. Among 153,977 students, no blindness was found related to trachoma. Trachoma was diagnosed in 8029 children (5.2%). In 87 schools clinical trachoma prevalence was higher than 5%. OCTI was confirmed in 2073 of 6823 trachoma diagnosed children (30.4%). Clinical trachoma prevalence was higher among females than males (p < 0.001), but gender comparison showed no statistical difference in the prevalence of OCTI (p = 0.077). Age and clinical trachoma (r = -0.014; p < 0.001) or OCTI (r = -0.026; p = 0.031) prevalence were negatively correlated. Clinical trachoma was different in different districts and counties (p < 0.001). Trachoma warrants close attention in Shanghai migrant children because the condition remains endemic in some schools.