Background In China, the pneumococcal conjugate vaccine (PCV7) and the pneumococcal polysaccharide vaccine (PPSV23) are not offered under the government’s Expanded Program on Immunization and are instead administered for a fee. PCV7 is more effective and covers more serotypes associated with invasive disease in children, but is also more expensive, than PPSV23. Because of their expense, there is concern that these vaccines, especially PCV7, have low uptake particularly among non-locals, migrants from outside of Shanghai. This paper characterizes the differential coverage of PCV7 and PPSV23 between locals and non-locals in Shanghai, and illustrates coverage trends over time. Methods In this retrospective cohort study, children born between 2005 and 2011 were sampled from the Shanghai Immunization Program Information System. Bivariate and multivariable analyses examined the relationships between demographic characteristics, residency status (non-locals vs locals), and vaccination coverage. Results PPSV23 coverage (29.8 %) among children over 2 years of age was higher than PCV7 coverage (10.1 %) for locals and non-locals. Uptake of PCV7 increased substantially after children were 2 years of age. Overall, non-local populations had higher PPSV23 coverage (OR: 1.34; 98 % CI: 1.22, 1.46) but lower PCV7 coverage (OR: 0.617, 98 % CI: 0.547, 0.695) than locals. Conclusions There is a need for increasing overall pneumococcal coverage in Shanghai children, particularly with the more effective PCV7 vaccine. Morbidity and mortality due to invasive pneumococcal disease for children <1 year of age are unlikely to be mitigated if the current age-related vaccination patterns are not improved.