Leptospirosis is a neglected zoonosis caused by a pathogenic spirochete, Leptospira interrogans. The mode of infection in humans is through an abrasion in human skin or the conjunctiva and mucous membrane. Infected patients usually show different symptoms resembling bacterial or viral infections such as the flu. Hence, diagnosing leptospirosis in the early stage is complex, and can be easily confused with other infections. A strategical pathway was developed to analyze the hypothetical proteins in L. interrogans and unveil their potential as diagnostic markers. Subcellular localization tools such as PSORTb, CELLO, SOSUI-GramN, and ProtCompB were used to segregate the outer membrane and surface proteins from the overall pool of hypothetical proteins. The shortlisted proteins were checked for their virulency, and antigenicity through tools such as VirulentPred, and VaxiJen, respectively. Proteins with the highest scores were fed into ElliPro which predicted both linear and discontinuous epitopes in each protein. Proteins with many epitopes were further analyzed with BepiPred 3.0, which provided the epitope probability for each protein’s amino acid. Epitope probability of the potential proteins was compared with the standard diagnostic marker, LipL32. The comparison revealed that a protein (UniProt ID D4YW28) has better immunogenic potential than the gold standard marker, LipL32. In conclusion, this protein can be used as a diagnostic marker for the detection of leptospirosis and it will also serve as a better vaccine candidate.