Background: Post-acute sequelae of SARS-CoV-2 infection (PASC) affects patients after recovering from acute coronavirus disease 2019 (COVID-19). This study investigates the impact of SARS-CoV-2 vaccination on PASC symptoms in children in Taiwan during the Omicron pandemic. Methods: We enrolled children under 18 years with PASC symptoms persisting for more than 4 weeks. Data collected included demographics, clinical information, vaccination status, and symptom persistence. We used logistic regression models to compare symptoms in the acute and post-COVID-19 phases and to assess the association between vaccination and these symptoms. Results: Among 500 PASC children, 292 (58.4%) were vaccinated, 282 (52.8%) were male, and the mean (SD) age was 7.6 (4.6) years. Vaccinated individuals exhibited higher odds of experiencing symptoms in the previous acute phase, such as cough (adjusted odds ratio [AOR] = 1.57; 95% confidence interval [CI]: 1.02–2.42), rhinorrhea/nasal congestion (AOR = 1.74; 95% CI: 1.13–2.67), sneezing (AOR = 1.68; 95% CI: 1.02–2.76), sputum production (AOR = 1.91; 95% CI: 1.15–3.19), headache/dizziness (AOR = 1.73; 95% CI: 1.04–2.87), and muscle soreness (AOR = 2.33; 95% CI: 1.13–4.80). In contrast, there were lower odds of experiencing abdominal pain (AOR = 0.49; 95% CI: 0.25–0.94) and diarrhea (AOR = 0.37; 95% CI: 0.17–0.78) in children who had received vaccination during the post-COVID-19 phase. Conclusions: This study revealed clinical features and vaccination effects in PASC children in Taiwan. Vaccination may reduce some gastrointestinal symptoms in the post-COVID-19 phase.