Background: Democrats are more likely to be vaccinated for COVID-19 than Republicans. It is unknown if political polarization surrounding the COVID-19 vaccine has affected flu vaccine uptake. The purpose of this study is to examine the partisan differences in annual flu vaccine uptake before and after the COVID-19 pandemic. Methods: This study uses longitudinal panel survey data from the Understanding America Study (UAS), spanning from 2015 to 2024. Using self-reported flu vaccination and partisanship over time, I estimate the odds ratios of flu vaccination for partisan groups before the COVID-19 pandemic, during the pre-vaccination phase of the COVID-19 pandemic, and after the rollout of the COVID-19 vaccine. Results: In pre-COVID years, the predicted probability of flu vaccination was 0.54 ([0.52,0.56], P < .000) among Republicans and 0.63 ([0.61,0.64], P < .00) among Democrats. After the roll-out of the COVID-19 vaccine, the average flu vaccination probability was 0.44 ([0.43,0.46], P < .00) among Republicans and 0.61 ([0.59,0.62], P < .00) among Democrats. Conclusions: The COVID-19 pandemic increased the partisan gap in annual flu vaccination. Researchers should continue to investigate if the partisan gap in other types of vaccinations has grown post-COVID. Practitioners may need to tailor their flu vaccine messaging to vaccine-hesitant political demographics.