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In hybrid seed production program based on three-line system, the use of fertility restorer line with desirable specific combining ability carrying fertility restoration (<em>Rf</em>) genes is indispensible. In this research, fertility restoration locus <em>Rf3</em> was transferred into CMS line ‘Neda-A’ using marker-assisted backcrossing (MAB) method and simultaneously its effect on pollen and panicle fertility of recipient line was evaluated in each generation. For transferring the locus, a single F₂ plant (derived from ‘Neda-A’ x ‘IR36’ cross) was selected based on <em>Rf3</em>-linked three markers (RM1, RM3233 and RM3873) and backcrossed to ‘Neda-A’ (as the recurrent parent). The BC₁ progenies were screened for <em>Rf3</em>-linked markers and also phenotyped and subsequently screened for 15 background SSR markers. Only two BC₁ plants with donor dominant allele at all three loci showed high panicle fertility (65% and 50%). BC₂ progenies were developed after backcrossing these two plants to recurrent parent. Among BC₂ progenies, a single plant having a higher fertility was self-pollinated and 170 resultant BC₂F₂ plants were screened with 3 foreground <em>Rf3</em>-linked markers (RM1, RM3233 and RM3873) and also evaluated in terms of seed setting. Seven plants were identified with a higher rate of recurrent parent genome (91.1% to 98.5%) and in complete homozygote state at three <em>Rf3</em>- linked markers. These plants had a high pollen and panicle fertility (75% to 97%), indicating that with increasing homozygosity of <em>Rf3</em> locus, fertility restoration to WA cytoplasmic male sterility in the genetic background of CMS recipient line was further enhanced. Therefore, it can be concluded that <em>Rf3</em> locus has an interaction to WA cytoplasmic male sterility in favor of increasing the rice pollen and panicle fertility, and hence it can be utilized along with other restoring fertility genes in hybrid seed production program of rice. <em> </em>