A 6-year-old boy was referred for evaluation because he had several vomiting episodes, from the age of 2 years, following short-neck clam ingestion. He tested negative for short-neck clam-specific IgE just before visiting our hospital, and he was not allergic to other foods or shellfish. The patient had low levels of short-neck clam-specific IgE (1.04 UA/ml), and the skin prick test was positive for short-neck clam (4 mm). The lymphocyte stimulation test was positive (5305 counts per min (cpm), stimulation index (SI) =1211%) and the patch test was positive for short-neck clam ingestion. An oral challenge test with boiled short-neck clam induced abdominal pain and vomiting 2 h after ingestion, and the patient presented with increased peripheral leukocytes after 6 h. He was therefore diagnosed with food protein-induced enterocolitis syndrome (FPIES) due to short-neck clam ingestion. To our knowledge, this is the first case report of FPIES induced by the intake of shellfish.