Pre-harvest sprouting (PHS) is a major abiotic factor that adversely affect wheat production and quality, thus limiting farmers’ income. We conducted a genome-wide association study (GWAS) and genomic prediction (GP) for PHS tolerance in wheat using sprouting score (SS), falling number (FN) and grain color (GC) as parameters. GWAS panel consisting of 190 accessions was phenotyped for three parameters over two years and genotyped with 9,904 polymorphic SNP markers. GWAS for main-effect QTNs (M-QTNs) was conducted using the following three models: CMLM, SUPER, and FarmCPU. A total of 171 M-QTNs (CMLM=47; SUPER=70; FarmCPU=54) were identified, suggesting differences in efficiencies of the three models. Epistatic interactions analysis using PLINK v1.07 led to the identification of 15 of epistatic QTNs (E-QTNs) involved on 20 epistatic interactions. The M-QTNs present on 19 chromosomes explained 5.9% to 7.9% phenotypic variation. A total of 26 PHS-responsive genomic regions each of 5 Mb on 16 wheat chromosomes demarcated by us that contained previously mapped QTLs, MTAs, cloned genes as well as M-QTNs reported by us, thus validating our results. These loci are assumed to be in LD. As many as 20 novel, definitive and stable QTNs were recommended for use in marker-assisted recurrent selection for improvement of PHST. Candidate genes associated with different QTNs revealed a major role in abscisic acid (ABA) signaling pathway in PHS tolerance. GP accuracies (based on cross-validation approach) using three different models range from 0.41 to 0.55, which are comparable to previous studies. Present study improved our understanding of the genetic architecture, provided novel genomic resources for wheat breeding and underlined future potential of GP for PHST in wheat.