The use of rainwater harvesting tanks to supply human water needs is an old and sustainable practice. In the case of covering irrigation demand in greenhouse agriculture, the potential is huge. Still, the relative research worldwide is low, while it is nearly absent in Greece. In this study, the rainwater harvesting tank size for irrigation use of greenhouse tomato cultivation was investigated by applying a daily water balance model in three regions of Crete Island (Greece) with significant greenhouse areas. Daily rainfall data from three representative rainfall stations of the study areas characterized by different rainfall regime for a 12-year time series were used. Additionally, the daily irrigation water needs for a tomato crop during an 8-month cultivation period were used. The greenhouse roof was defined as catchment area of the rainwater harvesting system and greenhouse areas of 1000, 5000 and 10,000 m2 were studied. In all areas examined, a tank of 30–100 m3 per 1000 m2 of greenhouse area could reach approximately 80–90% reliability. Higher values of reliability (reaching 100%) could be achieved mainly with covered tanks. Tank size for 100% reliability in covered tanks, ranged from 200 m3 (per 1000 m2 of greenhouse area) in the study area with high mean annual rainfall depth (974.24 mm) and moderate mean longest dry period (87.67 days), to 276 m3 (per 1000 m2 of greenhouse area) in the study area with relatively low mean annual rainfall depth (524.12 mm) and high mean longest dry period (117.42 days). For uncovered tanks, a 100% reliability value could be reached only with a tank size of 520 m3 (per 1000 m2 of greenhouse area) in the study area with high mean annual rainfall depth and moderate mean longest dry period.