Ponkan (Citrus reticulate) and Tachibana (Citrus tachibana) contain large amounts of polymethoxyflavones (PMFs). To produce highly functional food with high potential, it is important to develop technologies to increase their PMF content. Nobiletin content of the flavedo changed in harvested ‘Ohta Ponkan’ fruits after ultraviolet (UV)-C irradiation and PMF content increased for only the first 2 days following irradiation. The effect of UV-C or UV-B irradiation on PMF content at each harvest time (UV-C, July to December; UV-B, July to September) was observed in Ponkan and Tachibana. We found that UV-C had the greatest impact earlier in the season. The effects of UV-B irradiation were similar to UV-C results. Therefore, it is beneficial to harvest early and extract PMFs from fruit 24 hours after UV-C irradiation.