A sensitive strategy to rapidly detect fipronil residues in eggs using multibranch gold nanoparticles (AuNPs) as the substrate of surface-enhanced Raman spectroscopy (SERS) was investigated in this study. Under optimized conditions, fipronil molecules preferentially deposited on the multibranch gold nanoparticles with preferential (111) facet-oriented growth due to its low surface energy. This anisotropic growth promoted the increase of SERS “hot spots”, inducing a huge enhancement of Raman signals of the fipronil. An external standard calibration method was employed for quantitative analysis, and the method was validated for linearity, sensitivity, repeatability and recovery. Good linearity were found in the concentration range of 10 ng/L~10 mg/L in fipronil acetone solution (R2 = 0.9916) and 8 × 10−5 mg/m2 to 0.8 mg/m2 on eggshells (R2 = 0.9906), respectively. The recovery rate based on acetone recovered fipronil on eggshells and in egg liquids was 80.13%~87.87%, and 81.34%~88.89%, respectively. The SERS assay was successfully used to monitor fipronil in eggs.