The leptin receptor (LEPR) is involved in central signaling for both energy homeostasis and reproduction. The present study investigates the association of the LEPR gene with the prolificacy of Black Bengal goat. Two single nucleotide polymorphisms (SNPs) in intron 3 and one SNP in exon 4 in the LEPR gene were identified by pooled DNA sequencing. The identified SNPs were genotyped by the direct sequencing method from 84 Black Bengal does. A synonymous mutation (Lysine > Lysine) was found as a polymorphism in exon 4. The effects of the different genotypes on litter size traits were estimated using linear models. Our results show that goats with heterozygous genotype AG at the loci g.104911A>G and g.105151A>G showed the highest prolificacy performance when compared with the other, homozygous genotypes. Dominance and additive effects were observed at the considered loci. No significant allele substitution effects were found for any locus. Our results indicate preliminarily that LEPR may have some association with prolificacy and could be a candidate gene to improve the prolificacy in goat.