Ethylene-responsive factors (ERFs) are important plant transcription factors (TFs) that regulate plant responses against various abiotic stresses. However, little information of ERF genes involved in abiotic stress is available in petunia (Petunia ×hybrida). In this study, a petunia ERF gene, PhERF039, was cloned and functional analysis was performed. The quantitative PCR analysis revealed that PhERF039 was induced at the early stage of water deficit stress. Under-expression of PhERF039 (UE) exhibited rosette growth habit, higher number of branches, and delayed flowering compared to the wild type (WT). The UE petunia was evaluated under various volumetric water contents (θ): 0.25, 0.15, 0.10, or 0.05 m3·m-3 using an automated irrigation system. Transgenic plants did not delay plant wilting, but the θ for UE reached to the set point later than that for WT. A lower stomatal conductance was observed in UE than WT under all treatments. These results suggested that PhERF039 could be involved in plant responses under water deficit by regulating stomatal movements as well as branching pattern and flower development.