Green coffee bean extract (GCBE) and chlorogenic acids are known to be associated with weight loss. 5-O-caffeoylquinic acid (5-CQA) is the main form of chlorogenic acid in GCBE. This study investigated GCBE and 5-CQA’s molecular mechanisms on fat metabolism using Caenorhabditis elegans as a model system. Treatment of GCBE or 5-CQA reduced triglycerides level by 29% and 23%, respectively, compared to the control. GCBE and 5-CQA’s fat-lowering effects were dependent on sbp-1 (an ortholog of mammalian sterol-regulatory-element-binding protein) and daf-16 (an ortholog of mammalian Forkhead box O transcription factor). Additionally, the lipid-binding protein, FAR-6, was identified as a target for GCBE and 5-CQA, along with other proteins. Therefore, GCBE and 5-CQA’s fat-lowering effects are dependent on sbp-1, daf-16 and far-6 in C. elegans, which are involved in lipogenesis, energy homeostasis and lipid uptake, respectively. These results suggest that chlorogenic acids are most likely responsible for GCBE’s fat-lowering effects.