Irrigation scheduling and programming are very effective tools for efficient water use in a plant factory with artificial lighting (PFAL). In order to confirm optimal irrigation schemes for the production of cucumber scions and rootstocks in a PFAL, in this study, four different start points of irrigation were applied by measuring the weight of the plug tray to compare the growth of cucumber scions and rootstocks cultivated in a PFAL. Additionally, the growth characteristics of cucumber seedlings grafted with scions and rootstocks cultivated between in a greenhouse and in a PFAL were investigated. Although the growth of cucumber scions and rootstocks was highest when irrigation was conducted at 70% of water content in a medium, the growth of grafted cucumber seedlings before and after transplanting was not significantly different among the irrigation treatments in a PFAL. However, water use efficiency (WUE) during cucumber scions and rootstock production in a PFAL was higher at 60% than at 70%. Considering seedling growth and the efficiency of irrigation such as WUE and irrigation schedule, the optimal start point of irrigation during the production of cucumber scions and rootstocks in a PFAL was determined as 60% of water content in a medium. When the optimal irrigation regime was applied to the production of cucumber scions and rootstocks in a PFAL, the morphological characteristics of cucumber scions and rootstocks cultivated in a PFAL were more suitable for grafting compared with that of the cucumber scions and rootstocks cultivated conventionally in a greenhouse. The favorable environmental conditions during the cultivation of cucumber scions and rootstocks in a PFAL also positively affected the flowering response of cucumber grafted seedlings after transplanting.