Streptococcus pneumoniae is one of the leading causes of childhood morbidity and mortality globally. The study determined the antibiotic susceptibility profile and molecular serotyping of encapsulated S. pneumoniae isolated from the blood of 100 under 5 years old children presented at the children's clinic of the Mother and Child Hospital Akure, Nigeria. The S. pneumoniae isolates were identified using standard microbiological techniques. Antibiotic susceptibility test included the Kirby-Bauer disc diffusion method. The detection of the strain serotypes by polymerase chain reaction (PCR) technique was conducted and the data derived from the study were statistically analysed. A total of 16 (16%) encapsulated S. pneumoniae strains were identified. All the 16 isolates were resistant to penicillin, cloxacillin, tetracycline and erythromycin. The isolates were all multi-resistant to the antibiotics tested. Serotypes 6B, 14 and 19F were detected. The study presents the baseline report of serotype 14 detection at the study centre. The continuous monitoring of serotype distribution and antibiotic susceptibility in this population will assist immensely in future preventive and treatment strategies.