Introduction: The post-COVID-19 syndrome is a clinical entity characterized by the manifestation of signs and symptoms that develop after the acute phase of COVID-19, which persist for a duration of more than 12 weeks and are not explained by any alternative diagnosis. It has been observed that individuals with pre-existing chronic diseases, including cardiovascular and pulmonary diseases, are at a greater risk of developing post-COVID-19 syndrome. The Charlson Comorbidity Index (CCI) is a useful tool employed to evaluate the burden of comorbidities and predict the prognosis of patients with post-COVID-19 syndrome. The present study aims to assess whether the burden of comorbidities, evaluated using the CCI, correlates with post-COVID-19 syndrome. Materials and Methods: Between 21 April 2020 and 15 May 2023, we enrolled all consecutive outpatients with previous COVID-19 admissions to a post-acute day-hospital service three months after a negative SARS-CoV-2 molecular test. We assessed age, sex, BMI, acute COVID-19 and post-COVID-19 signs, and symptoms and calculated CCI according to its current definition. Post-COVID-19 syndrome was defined as the persistence of at least one sign or symptom lasting more than 12 weeks after COVID-19 resolution and not explained by an alternative diagnosis. The relationship between post-COVID-19 and CCI was explored first with the chi-squared test, then with different binary logistic regression models. We considered significant values of p lower than 0.05. Results: We obtained a cohort of 3636 patients and observed a significant association between the number of post-COVID-19 symptoms and CCI. Patients developing post-COVID-19 were more commonly affected by a greater burden of comorbidities. Patients with at least one CCI point had an increased risk of post-COVID-19 syndrome (OR:2.961; 95%CI: 2.269–3.863; p < 0.0001), which increased further for CCI ≥ 4 (OR:6.062; 95%CI: 3.163–11.618; p < 0.0001). Conclusions: Patients affected by post-COVID-19 show a greater clinical complexity and a larger burden of comorbidities, synthesized by a higher CCI; moreover, a higher CCI seems to correlate with an increasing post-COVID-19 risk, being the presence of ≥1 or ≥4 CCI points associated with a 3-fold and 6-fold increased risk of post-COVID-19 syndrome, respectively.