Electrocoagulation (EC) with a zinc anode can effectively remove perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) from water. Besides hydrophobic interactions between PFOA/PFOS and zinc hydroxide flocs, aeration is another crucial factor determining PFOA/PFOS removal in EC. This study examined how aeration (in terms of bubble sizes and flow rates) could impact PFOA/PFOS removal in EC. Both bubble sizes (coarse vs. fine) and airflow rates (7.9, 9.4, and 11.0 mL per sec) were critical for PFOA removal and zinc hydroxide floc generation. EC aerated with fine bubbles had 14–21% higher PFOA removal efficiency than EC aerated with coarse bubbles. PFOA removal by EC with a high airflow (11.0 mL per sec) was 19% higher than EC with a medium airflow (9.4 mL per sec), or 31–37% higher than EC with a low airflow (7.9 mL per sec). These results indicate that fine bubbles and high airflow rates are more beneficial for PFOA removal, likely due to a greater air–water contact area and turbulence. The EC with coarse bubbles produced zinc hydroxide flocs with 29–34% greater Brunauer–Emmett–Teller (BET) surface area and 18% greater mass. However, the BET surface area and mass of the flocs were not critical for PFOA removal. The impacts of aeration on PFOS removal in EC were not significant.