The study compared the risk of post-acute sequelae (PAS) after SARS-CoV-2 and influenza infection in 74,738 cases of COVID-19 and 18,790 cases of influenza diagnosed in the Kaiser Permanente system in Southern California from September 1, 2022, to December 31, 2023. The risk of PAS in any clinical setting was only slightly higher for COVID-19 in the 31–90 day period (aHR = 1.04 [95% CI: 0.99, 1.09]; difference 0.6 events per person-month) and even less at 91–180 days (aHR = 1.01 [0.97, 1.06]; difference 0.4 events per 100 person-months). For COVID-19 cases hospitalized in the acute phase, the risk of severe PAS requiring hospitalization was higher (aHR = 1.31 [1.07, 1.59] at 31–90 days and 1.24 [1.03, 1.49] at 91–180 days). This risk was reduced in patients with antiviral treatment, vaccination before infection, or no hospitalization in the acute phase. The analysis included only PAS associated with health care utilization, not patient-reported symptoms or quality of life. The findings suggest that for non-severe cases, the risk of PAS after COVID-19 is similar to that after influenza, but there remains a higher risk of serious conditions after hospitalized COVID-19.