Background: Northern corn leaf blight (NCLB) of maize caused by Exserohilum turcicum is a serious foliar disease. Resistance to NCLB is complexly inherited and the highly significant genotype x environment interaction effect makes selection of resistant genotypes difficult through conventional breeding methods. Hence an attempt was made to identify the genomic regions associated with NCLB resistance and perform genomic selection (GS) in two F2:3 populations derived from the crosses CM212 × MAI172 (Population-1) and CM202 × SKV50 (Population-2). Results: Two populations, each comprising of 366 progenies, were phenotyped at three different locations in the disease screening nurseries. Linkage analysis using 297 polymorphic SNPs in Population-1 and 290 polymorphic SNPs in Population-2 revealed 10 linkage groups spanning 3623.88cM and 4261.92cM with an average distance of 12.40 cM and 14.9 cM, respectively. Location-wise and pooled data across locations indicated that QTL expression was population and environment specific. The genomic prediction accuracies of 0.83 and 0.79 were achieved for NCLB Population 1 and Population 2, respectively. The resistant progenies from both populations were advanced to derive inbred lines and crossed with four different testers in line x tester mating design to test for their combining ability. High overall general combining ability was exhibited by 21 inbred lines. Among crosses 48 % were assigned high overall specific combining ability status. Out of 136 single crosses, seven recorded significant positive standard heterosis over the best check for grain yield. The clustering pattern of inbred lines developed from the two populations revealed high molecular diversity. Conclusions: In this study, comparatively better genomic prediction accuracies were achieved for NCLB and the worth of F3 progenies with high genomic predictions was proved by advancing them to derive inbred lines and establishing their higher combining ability for yield and yield related traits.