Food allergy has become a global concern. Spleen tyrosine kinase (SYK) inhibitors are promising therapeutics against allergic disorders. In this study, a total of 300 natural phenolic compounds were firstly subjected to virtual screening. Sesamin and its metabolites, sesamin monocatechol (SC-1) and sesamin dicatechol (SC-2), were identified as potential SYK inhibitors, showing high binding affinity and inhibition efficiency towards SYK. Compared with R406 (a traditional SYK inhibitor), sesamin, SC-1, and SC-2 had lower binding energy and inhibition constant (Ki) during molecular docking, exhibited higher bioavailability, safety, metabolism/clearance rate, and distribution uniformity ADMET predictions, and showed high stability in occupying the ATP-binding pocket of SYK during molecular dynamics simulations. In anti-dinitrophenyl-immunoglobulin E (Anti-DNP-IgE)/dinitrophenyl-human serum albumin (DNP-HSA)-stimulated rat basophilic leukemia (RBL-2H3) cells, sesamin in the concentration range of 5–80 μmol/L influenced significantly the degranulation and cytokine release, with 54.00% inhibition against β-hexosaminidase release and 58.45% decrease in histamine. In BALB/c mice, sesamin could ameliorate Anti-DNP-IgE/DNP-HSA-induced passive cutaneous anaphylaxis (PCA) and ovalbumin (OVA)-induced active systemic anaphylaxis (ASA) reactions, reduce the levels of allergic mediators (immunoglobulins and pro-inflammatory cytokines), partially correct the imbalance of T helper (Th) cells differentiation in the spleen, and inhibit the phosphorylation of SYK and its downstream signaling proteins, including p38 mitogen-activated protein kinases (p38 MAPK), extracellular signal-regulated kinases (ERK), and p65 nuclear factor-κB (p65 NF-κB) in the spleen. Thus, sesamin may be a safe and versatile SYK inhibitor that can alleviate IgE-mediated food allergies.