•The fly ash source has a significant effect on fly ash-based geopolymer concrete compressive strength.•The particle size distribution (PSD) has a direct effect on the compressive strength.•The fly ash source has a significant effect on fly ash-based geopolymer concrete microstructure.•The finer the fly ash particle size distribution, the more significantly permeable void ratio was reduced.•Fewer microcracks were observed when finer fly ash was used. Geopolymer concrete has demonstrated promising mechanical and microstructural properties in comparison with conventional concrete; however, the variability found in fly ash sources and properties may be an obstacle to implementation. To better understand this variability, this study investigates the effects of particle size distribution and fly ash source on the mechanical and microstructural properties of fly ash-based geopolymer concrete. Two fly ash sources were studied including ordinary McMeekin and Wateree Station fly ash. McMeekin fly ash has three different fly ash particle grades, including the ordinary McMeekin fly ash (38.8 µm), Spherix 50 (17.9 µm), and Spherix 15 (4.78 µm). The Wateree Station is a thermally beneficiated fly ash, while McMeekin is a STAR Processed fly ash. A mixture of silica fume, sodium hydroxide, and water was used as an activating solution. The microstructure of fly ash-based geopolymer paste was observed using SEM. The density, absorption and permeable void ratios were estimated based on ASTM C642. Test results indicate that the resulting compressive strength is linearly affected by the average particle size distribution. The compressive strength of geopolymer concrete was decreased when McMeekin fly ash was used. In addition, the permeable void ratio and absorption after immersion ratio were decreased as a smaller particle size of fly ash such as Spherix 15 (4.78 µm) was used. The fly ash source influences the permeable voids, apparent density, bulk density, and absorption after immersion ratio.