Objectives: Fixation preference testing is widely used to detect amblyopia, particularly in preverbal children. Pattern electroretinogram (pERG) is an electrophysiological test which is a sensitive indicator of macular function. The aim of this study was to investigate the relationship between fixation preference and macular function on pERG in children with strabismus. Materials and Methods: The study included 11 children with strabismus. All underwent ophthalmological examination including fixation preference by binocular fixation pattern test, best corrected visual acuity (BCVA) assessment, and pERG. Results: The mean age of the patients was 10.09±1.18 years. All patients had unilateral fixation. The mean BCVA was 0.85±0.17 in preferred and 0.48±0.19 in non-preferred eyes (p=0.003). The mean p50 amplitude was 6.07±2.06 μV in preferred and 5.29±2.20 μV in non-preferred eyes (p=0.203), and the mean N95 amplitude was 8.27±2.86 μV and 8.03±3.24 μV respectively (p=0.594). BCVA was correlated with p50 and N95 amplitudes in the non-preferred eyes (p=0.023 and p=0.014). Interocular BCVA difference was correlated with interocular P50 amplitude difference (r=0.688, p=0.019). Conclusion: Although amblyopia is typically considered a cortical phenomenon, future larger studies are needed to investigate the relationship between fixation preference and macular electrophysiological function.