Insect infestation can adversely affect tomato (Solanum lycopersicum L.; Solanaceae) development and yield. Fruit flies (Diptera: Tephritidae) are a serious pest of tomato, and are spreading to areas where they were not previously found. This study was undertaken to determine if tephritid fruit flies were present, which species were most abundant, how tomato cultivars responded, and what amount of damage occurred in the Eastern Himalayas of India during May 2014 and 2015. Mature and ripe fruit (n = 20) per cultivar were picked at random from 12 cultivars at weekly intervals to assess percentage of infestation, fly species composition, larval infestation, pupal mortality, adult emergence, and sex ratio during 2 seasons. Seasonal fluctuation of male adults of Zeugodacus tau (Walker) (Diptera: Tephritidae) in tomato was studied by installing 3 modified clear traps, made from plastic bottles, that were baited with 0.5 mL Cue-lure and the insecticide dichlorovos 76% EC (Nuvan^®). Survey and subsequent identification confirmed the presence of Z. tau in tomato in the Himalayas of India. This is the first report of the insect in the province, and of population outbreaks resulting in serious damage to tomato in India. Among fruit fly species present on tomato, Z. tau was more abundant (71.4–96.4%) in all geographical regions of Mizoram, India, than were Bactrocera correcta (Bezzi), B. dorsalis (Hendel), and B. latifrons (Hendel), which ranged from 3.6 to 28.6%. The highest percentage of infestation was in Champhai (72.7 ± 6.7%) and Kolasib (80.7 ± 3.5%) and the lowest in Mamit (14.7 ± 4.8%) and Serchhip (19.3 ± 4.7%). Cultivar influenced pupal mortality and adult emergence of Z. tau. Seasonal fluctuation of Z. tau males on tomato varied; the greatest numbers were trapped during May and Dec. Occurrence of Z. tau at high population densities was associated with high levels of damage and could lead to high economic losses in tomato fruit production.