Bulb onion (Allium cepa L.) is an economically valuable vegetable crop in the United States. Onion production is threatened by onion thrips, which are the vector for Iris yellow spot virus, which is the causal agent of Iris yellow spot (IYS). New Mexico State University (NMSU) breeding lines 12-236, 12-238, 12-243, and 12-337 have exhibited fewer IYS disease symptoms in the field; however, little is known about the effects of the disease on the photosynthesis rate (Pn). We hypothesized that these NMSU breeding lines would have a higher Pn than IYS-susceptible cultivars Rumba and Stockton Early Yellow. To test this hypothesis, a field study was conducted for 3 years at NMSU, and Pn was measured five times throughout each season at 2-week intervals. During bulb development and maturation, which occurred at 10 and 12 weeks after transplanting, all NMSU breeding lines exhibited a higher Pn when compared with that of an IYS-susceptible cultivar. Pn was highest at the end of the vegetative growth stage and decreased as bulbs approached maturation for all cultivars. Additionally, a high Pn at 10 and 12 weeks after transplanting coincided with high bulb weight at harvest. NMSU breeding lines have increased Pn compared with that of IYS-susceptible cultivars and resulted in larger and more marketable bulbs. These results indicate that maintaining Pn may be related to reduced IYS symptom expression of onion.