Tuberculosis (TB) which is caused by Mycobacterium tuberculosis infects primarily the lungs but it also affects other parts of the body. Tuberculous meningitis (TBM) is the most severe form of TB and has the highest mortality and morbidity rate compared to other forms of TB. It is common in young children and HIV-infected patients, but is also seen in adults. Despite anti-tuberculosis treatment, TBM is still a major cause of death and neurological sequelae as treatment given to the patients is often delayed. Early diagnosis is challenging due to the non-specific symptoms of TBM and the low number of tubercle bacilli in cerebrospinal fluid (CSF). Until now, there is no established diagnostic method that can rapidly detect M. tuberculosis in TBM patients with high sensitivity and specificity. The emergence of drug resistant M. tuberculosis strains further complicates the diagnosis and treatment regimen of TBM. This review summarizes challenges of the currently used diagnostic methods and the potential future use of molecular diagnostic methods for TBM.