Heading date is a critical trait that determine the regional adaptability and grain productivity in many crops. Although rice is a facultative short-day plant, its domestication led to the Ghd7-Ehd1-Hd3a/RFT1 pathway to adapt for long-day conditions (LDs). The formation of ‘florigen activation complex’ (FAC) containing florigen Hd3a has been elucidated. However, the molecular composition of FAC with RFT1 for long-day flowering are unclear. We show that RFT1 forms a ternary FAC with 14-3-3 proteins and OsFD1 for flowering under LDs. The calcineurin B-like-interacting protein kinase, OsCIPK3, directly interacts with OsFD1 and phosphorylates OsFD1, which could facilitate FAC to localize in the nucleus. Mutation in OsCIPK3 results in a late heading date under LDs but normal heading date under short-day conditions (SDs). Our results suggest that OsCIPK3 phosphorylates OsFD1 for RFT1-containing FAC formation to initiate flowering in rice under LDs.