The timely transition from vegetative to reproductive growth is vital for reproductive success in plants. It has been suggested that messenger RNA 3′-end processing plays a role in this transition. Specifically, two autonomous factors in the Arabidopsis thaliana flowering time control pathway, FY and FCA, are required for the alternative polyadenylation of FCA pre-mRNA. In this paper we provide evidence that Pcf11p-similar protein 4 (PCFS4), an Arabidopsis homologue of yeast polyadenylation factor Protein 1 of Cleavage Factor 1 (Pcf11p), regulates FCA alternative polyadenylation and promotes flowering as a novel factor in the autonomous pathway. First, the mutants of PCFS4 show delayed flowering under both long-day and short-day conditions and still respond to vernalization treatment. Next, gene expression analyses indicate that the delayed flowering in pcfs4 mutants is mediated by Flowering Locus C (FLC). Moreover, the expression profile of the known FCA transcripts, which result from alternative polyadenylation, was altered in the pcfs4 mutants, suggesting the role of PCFS4 in FCA alternative polyadenylation and control of flowering time. In agreement with these observations, using yeast two-hybrid assays and TAP-tagged protein pull-down analyses, we also revealed that PCFS4 forms a complex in vivo with FY and other polyadenylation factors. The PCFS4 promoter activity assay indicated that the transcription of PCFS4 is temporally and spatially regulated, suggesting its non-essential nature in plant growth and development.