Background: Pneumococcal conjugate vaccines (PCVs) are the most expensive component of the routine immunisation schedule in Gavi-supported countries. As countries transition out of Gavi support, PCV programmes are at risk. We assessed whether immunogenicity was non-inferior after fractional doses of PCV10 (GlaxoSmithKline plc.) or PCV13 (Pfizer Inc.), when compared to full doses, and analysed vaccine serotype (VT) carriage prevalence. Methods: 2100 healthy infants were enrolled and randomised into seven equal-sized trial arms. Doses were delivered in the 2p+1 schedule (6, 14 weeks and 9-12 months) in six trial arms: A) Full dose PCV13, B) 40%-PCV13, C) 20%-PCV13, D) Full dose PCV10, E) 40%-PCV10, F) 20%-PCV10. Participants in the seventh trial arm received full dose PCV10 at 6, 10 and 14 weeks. Immunogenicity was assessed 4-weeks post-prime and 4-weeks post-boost. Carriage was assessed at 9 and 18 months of age. Results: In the per-protocol analysis, 40%-PCV13 met the non-inferiority criteria for 12/13 serotypes post-prime and 13/13 serotypes post-boost. 20%-PCV13 met the criteria for 9/13 serotypes post-prime and 10/13 serotypes post-boost. 40%-PCV10 met the criteria for 8/10 serotypes post-prime and 6/10 serotypes post-boost. 20%-PCV10 met the criteria for 7/10 serotypes post-prime and 1/10 serotype post-boost. Conclusions: A 3-dose schedule of 40%-PCV13 met the non-inferiority criteria at both timepoints and could be implemented by using 4-dose UNICEF vials as 10-dose vials. A 3-dose schedule of 40%-PCV13 would cost UNICEF 3.30 USD and represents the most affordable, effective PCV schedule option currently available for countries transitioning out of Gavi-support. ClinicalTrials.gov ID:NCT03489018.