Although maternal pertussis vaccination is recommended, uptake is suboptimal in New Zealand (NZ), despite full funding in general practice and hospitals. We determined whether funding maternal pertussis vaccination in community pharmacy increases its uptake. Pertussis vaccination during pregnancy was compared between non-contiguous, demographically similar regions of NZ. The pertussis vaccine was funded at pharmacies from Nov 2016 in one NZ region (Waikato), but not in comparator regions (Northland, Hawkes Bay). Vaccinations during pregnancy were determined from the National Immunisation Register, general practice and pharmacy claims data, and a maternity database. Comparisons were made using adjusted odds ratios (OR) and 95% confidence intervals (CI) for Nov 2015 to Oct 2016 versus Nov 2016 to Oct 2019. The odds of pregnancy pertussis vaccination increased in the post-intervention versus pre-intervention period with this increase being larger (p = 0.0014) in the intervention (35% versus 21%, OR = 2.07, 95% CI 1.89–2.27) versus the control regions (38% versus 26%, OR = 1.67, 95% CI 1.52–1.84). Coverage was lower for Māori versus non-Māori, but increased more for Māori in the intervention versus control regions (117% versus 38% increase). It was found that funding maternal pertussis vaccination in pharmacy increases uptake, particularly for Māori women. Measures to increase coverage should include reducing barriers to vaccines being offered by non-traditional providers, including pharmacies.