Acute respiratory infections (ARIs) occur throughout life but are most common during the first two years. They are the leading cause of death in children aged under 5-years, and the sixth leading cause of death for all ages globally. One of the most common bacterial pathogens responsible for ARIs is Streptococcus pneumoniae (Spn). The aim of this study was to investigate the dynamics of pneumococcal nasopharyngeal carriage using multilocus sequence typing (MLST) to determine the sequence types (ST) within a subset of pneumococcal-positive nasal swabs from children. A subset of pneumococcal positive swabs were selected from 19 children (isolated weekly over at least 4 weeks as part of the Brisbane-based Observational Research in Childhood Infectious Diseases birth cohort). PCR and sequencing of 7 pneumococcal MLST genes was performed using standard pneumococcal MLST primers. MLST analysis identified 15 distinct pneumococcal STs, with 4 STs (ST156, ST1373, ST63, ST1262) making up 62% of all swabs. Various patterns of pneumococcal carriage were seen in children over time. For example, subject 027 had Spn ST156 for three consecutive weeks, then the nasal swab collected three weeks later showed Spn ST1373, which persisted for 12 weeks. Subject 085 also had Spn ST1373 for three consecutive weeks. Subject IDs 015, 098 and 157 had colonisation with Spn ST63 for a combined total of 12 weeks, making it the second most prevalent ST after ST1373. Subject IDs 109 and 150 had 7 and 9 weeks of confirmed colonisation with Spn ST1262, respectively. Overall, our data suggests that pneumococcal carriage with the same strain persists over several weeks, although temporal shifts do occur in pneumococcal STs. The detailed analysis of pneumococcal carriage may aid the development of future treatment and prevention strategies.