In cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system, the male sterility might become fertile once the fertility restorer gene(s) is present. However, different restorer genes may represent levels of restorative ability in the three-line hybrid soybean breeding. In this study, the CMS line JLCMS84A and its restorer line JLR1 were used as female and male parents, respectively, to construct F2 population used for genetic mapping. Segregation analysis during R2 stage indicated a typical inheritance pattern of gametophytic CMS with fertility restorer being controlled by a single dominant gene. allocated The restorer gene was allocated using BSA-seq on chromosome 9 between SSR markers BARCSOYSSR_09_1151 and BARCSOYSSR_09_1183 with the distances of 0.6 cM and 0.5 cM, respectively. Based on the soybean reference genome ZH13 v2.0, this physical interval spans 522 kb between 41.152 to 41.674 Mb and hosts a novel restorer gene named Rf3. Out of 51 annotated genes in the target region, three genes (SoyZH13_09G151700, SoyZH13_09G152000 and SoyZH13_09G154200) are encoded for putative pentatricopeptide repeat (PPR) protein. By PCR amplification and Sanger sequencing of their full-length DNA sequences between the CMS line JLCMS84A and its restorer line JLR1, three SNPs and two InDels, which lead to frame-shift mutations in SoyZH13_09G152000, have been identified, while 47 SNPs in SoyZH13_09G154200 have been detected. Therefore, both genes were the strongest candidates for Rf3. These results lay a foundation for fine mapping and function identification, as well as marker-assisted selection of new restorer lines which contained this restorer gene.