Tuberculosis remains one of the most dreaded infectious diseases notwithstanding the availability of a number of anti-tuberculosis drugs. The recent rise of multidrug-resistant tuberculosis and its association with HIV infection poses a challenging health concern. Therefore, there exists a pressing requirement to identify novel drug targets and develop new anti-tuberculosis drugs that will be effective against multidrug-resistant-tuberculosis. Shikimate kinase is a novel and attractive drug target as it is vital for the survival of Mycobacterium tuberculosis but is absent in mammals. Hence, inhibitors designed against shikimate kinase will be specific to the pathogen and be least harmful to the host. Till date, no drug candidates are available against this target. The crystal structure of Mycobacterium tuberculosis shikimate kinase complexed with shikimate has been used to identify a dipeptide inhibitor using in silico structure-based design approach. The designed peptidic inhibitor has a predicted binding affinity of 5.5 nm which is 8000 times better than substrate shikimate and 10 times greater than the best suggested inhibitor. It is potent in both the known open and closed LID conformations of target protein. As small peptides are known to be non-toxic, this inhibitor could be a lead compound for development of specific anti-tuberculosis drugs.