Genetic evidence has implicated multiple pathways in eukaryotic DNA mismatch repair (MMR) downstream of mispair recognition and Mlh1-Pms1 recruitment, including Exonuclease 1 (Exo1)-dependent and -independent pathways. We identified 14 mutations in POL30, which encodes PCNA in Saccharomyces cerevisiae, specific to Exo1-independent MMR. The mutations identified affected amino acids at three distinct sites on the PCNA structure. Multiple mutant PCNA proteins had defects either in trimerization and Msh2-Msh6 binding or in activation of the Mlh1-Pms1 endonuclease that initiates excision during MMR. The latter class of mutations led to hyperaccumulation of repair intermediate Mlh1-Pms1 foci and were enhanced by an msh6 mutation that disrupted the Msh2-Msh6 interaction with PCNA. These results reveal a central role for PCNA in the Exo1-independent MMR pathway and suggest that Msh2-Msh6 localizes PCNA to repair sites after mispair recognition to activate the Mlh1-Pms1 endonuclease for initiating Exo1-dependent repair or for driving progressive excision in Exo1-independent repair. Display omitted •PCNA mutants disrupt Exo1-independent MMR by two mechanisms•Mutants either poorly bind Msh2-Msh6 or poorly activate the Mlh1-Pms1 endonuclease•Activation mutations are enhanced by loss of the interaction with Msh2-Msh6•Msh2-Msh6 promotes excision by localizing PCNA for Mlh1-Pms1 activation DNA mismatch repair (MMR) involves Exo1-dependent and -independent pathways for excision of the mispair. Using S. cerevisiae, Goellner et al. identified mutations in the gene encoding PCNA specific to the Exo1-independent pathway and show that PCNA binding to Msh2-Msh6 and activation of the Mlh1-Pms1 endonuclease are critical to Exo1-independent MMR.