Mycobacterium tuberculosis (MTB) strains were isolated from cerebrospinal fluids collected from individual tuberculous meningitis (TBM) patients from 1996 to 2007 (n = 184) and characterised based on IS6110-restriction fragment length polymorphism (RFLP), spoligotyping, Mycobacterium interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) and large sequence polymorphisms (LSPs). Beijing strains were found to possess the highest transmissibility and proportion in clustered isolates. Beijing strain predomination and stability, at 56% of the genotypic proportion, as well as association with drug resistance in TBM patients, was demonstrated. The proportion of Beijing sublineages revealed that the modern Beijing sublineage showed an increasing trend, whereas the ancestral Beijing sublineage showed a decreasing trend across the three periods. In contrast, there were neither clustered nor multidrug-resistance (MDR) isolates from the Euro-American (EuA) lineage, and the lineage genotypic proportion trend was also decreased. Based on LSPs, only the Beijing, Indo-Oceanic and Euro-American lineages were identified from TBM patients in Thailand. TBM mortality rates were not associated with either drug resistance or significantly different among MTB lineages. This study may support the Beijing genotype strain as most pathogenic causing TBM, with the EuA lineage genotype as the most benign of the strain genotypes tested. The analysis of drug susceptibility also revealed the trend of increasing drug resistance, especially MDR, in TBM patients in Thailand.