The proper transition to flowering is a critical process for the success of plant reproduction and must be highly orchestrated. Nuclear Factor-Y subunit C (NF-YCs), which are closely related to histone H2A, exert diverse chromatin-mediated regulation over plant development events including flowering. However, the mechanisms by which NF-YCs regulate RNA polymerase II (Pol II) during gene transcription remain elusive. Here, we demonstrate that NF-YCs physically interact with EARLY FLOWERING 7 (ELF7), a core component of RNA Pol II-associated factor 1 complex (PAF1c), both in vitro and in vivo. We show that NF-YCs regulate flowering in an ELF7-dependent manner by repressing the expression of the floral repressor FLOWERING LOCUS M (FLM). Further analyses reveal that NF-YCs antagonize the binding of ELF7 to FLM chromatin, thereby suppressing ELF7-mediated RNA Pol II transcription at the FLM locus. Collectively, our findings uncover a novel chromatin-mediated regulatory mechanism in which NF-YCs, in association with ELF7, control the transcription of FLM to modulate flowering time.