Objective: To determine the antimicrobial susceptibility and serotypes of Neisseria (N.) meningitidis and Streptococcus (S.) pneumoniae in Sri Lankan patients. Methods: We retrospectively analyzed 11 blood culture specimens from suspected patients with invasive meningococcal disease and 26 S. pneumoniae clinical isolates. We tested 6 antimicrobials against N. meningitidis and 12 antimicrobials against S. pneumoniae. Meningococcal serogroup was determined by realtime PCR and Quellung serotyping was used for pneumococcal analysis. Results: N. meningitidis serogroup B was the most common in this study. Intermediate-susceptibility to penicillin was seen in 75.0% (6/8) of strains. Susceptibility to ciprofloxacin, levofloxacin and cotrimoxazole was 62.5% (5/8), 62.5% (5/8) and 87.5% (7/8), respectively. Excellent susceptibility was seen in cefotaxime and meropenem. In S. pneumoniae, the most common serotype was 19F in both invasive and non-invasive pneumococcal diseases. The majority of strains showed multidrug resistance. Penicillin non-susceptibility in non-meningeal strains were 13.6% and all meningeal strains were penicillin resistant. Erythromycin was highly resistant in both groups. Amoxicillin showed excellent susceptibility in non-invasive pneumococcal diseases strains. Linezolid, levofloxacin and vancomycin showed 100.0% susceptibility in all pneumococcal isolates. Conclusions: Implementation of vaccines should be considered, especially for children and high-risk populations. This may contribute to reducing pneumococcal and meningococcal invasive disease burden and help prevent emergence of antimicrobial resistant strains.