Fipronil and its metabolite fipronil sulfone, when found in some food products, such as eggs, have caused major public health concerns. In this study, we used gold nanorods (AuNRs) and graphene oxide (GO) nanocomposites to fabricate a layer-by-layer assembled three dimensional (3D) substrate for toxin detection by surface enhanced Raman scattering (SERS). The 4-layers of GO-AuNR 3D SERS substrate were optimized using rhodamine 6G. The optimized SERS substrate was used to detect fipronil and fipronil sulfone in spiked eggs. The obtained limit of detection was 10-8 M (∼4.4 ppb), which is below the maximum residue limit in Taiwan of 10 ppb. Egg samples spiked with fipronil (10-7 and 10-3 M) and fipronil sulfone (10-8 and 10-4 M) were measured and the maximum departure of the measured SERS intensity from the calibrated SERS intensity was ∼14%. Thus, a facile screening method for the detection of fipronil/fipronil sulfone in food-grade eggs by SERS is demonstrated.