Pre-harvest sprouting (PHS) is a phenomenon that causes substantial losses in the yield of cultivated Vigna and is mainly brought on by humid conditions. Although there is potential for genotypic PHS tolerance, this has not been thoroughly investigated in cowpea. The current study set out to understand the effects of several physiological and physical characteristics on PHS and to investigate the genetic variation for PHS tolerance in cowpea (Vigna unguiculata [L.] Walp.) germplasm. A diverse panel of 102 cowpea accessions was examined for seed and pod morphological characteristics, water imbibition by seeds and pods, and fresh seed germination to characterize the PHS trait. A wide variation for PHS was reported within cowpea accessions. Seed germination within pods, a key measure in assessing PHS tolerance, exhibited a wide range from 5 to 95%. Notably, six accessions (IC257422, IC338865, IC202837, EC004862, EC343036, IC259075) demonstrated PHS tolerance, with PHS values below 10%. Correlation analysis highlighted the positive influence of pod and seed water imbibition as well as fresh seed germination on PHS. Multivariate analysis further affirmed the positive association between PHS and water imbibition and fresh seed germination traits. Newly identified PHS tolerant accessions can be used in cowpea improvement programs to aid in the development of improved cowpea cultivars with PHS tolerance.