Introduction: The COVID-19 pandemic has exerted a profound global impact, extending beyond the acute phase to a condition known as long COVID, characterized by persistent symptoms following the initial infection. In Brazil, particularly in the Amazon region, the prevalence of long COVID remains high, with affected individuals exhibiting a wide range of multisystemic symptoms. This study aimed to investigate the clinical sequelae associated with long COVID, with a focus on the roles of vaccination and other contributing factors. Objectives: To assess the long-term sequelae of COVID-19 in residents of the Brazilian Amazon, comparing outcomes between vaccinated and unvaccinated individuals, as well as between those who were hospitalized and those who were not. The study also examined the relationship between symptom severity and time since infection and evaluated the effects of different vaccine types and the number of doses received. Materials and Methods: This cross-sectional, observational study was conducted between 2023 and 2024 and included 300 patients diagnosed with long COVID. Participants were stratified based on vaccination status, history of hospitalization, duration since acute infection, and symptom severity. Data on demographics and clinical presentation were collected through structured interviews and review of electronic medical records. Statistical analyses were performed using Jamovi software, employing appropriate inferential tests and multivariate logistic regression models. Results: Fatigue, headache, and muscle weakness were the most commonly reported symptoms, particularly among hospitalized individuals and those with higher symptom burden. Vaccination was associated with a reduction in symptom prevalence, with the most pronounced effect observed among recipients of the CoronaVac vaccine. Furthermore, a dose–response relationship was identified, wherein a greater number of vaccine doses correlated with decreased symptom frequency. Conclusion: Long COVID is a multifaceted condition marked by prolonged symptoms, especially among individuals with severe initial disease. Vaccination, particularly with multiple doses, was associated with reduced symptom burden. Nonetheless, fatigue and headache remained prevalent, underscoring the need for continued research into the underlying pathophysiology and development of targeted therapeutic strategies, particularly within the unique context of the Amazon region.