The coexistence of tuberculosis and other chronic diseases complicates disease management. Particularly, the lack of information on the difference in the prevalence of chronic diseases in tuberculosis based on age and gender can hinder the establishment of appropriate public health strategies. This study aimed to identify age- and gender-based differences in the prevalence of chronic diseases as comorbidities in patients with tuberculosis. An anonymized data source was established by linking the national health insurance claims data to the Korean national tuberculosis surveillance data from 2014 to 2018. The prevalence of chronic diseases was stratified by gender and age (age groups: ≤64, 65–74, and ≥75 years), and the differences in the prevalence of chronic diseases were analyzed by multinomial logistic regression and classified using the Charlson Comorbidity Index. A total of 148,055 patients with tuberculosis (61,199 women and 86,856 men) were included in this study. Among the patients aged ≥65 years, 48.2% were female and 38.1% were male. In this age group, the probability of chronic disease comorbidity was higher in female patients than in male patients. The prevalence of congestive heart failure and dementia as comorbidities in patients with tuberculosis increased more drastically with age in women than in men. Thus, the present study confirmed gender and age differences in the distribution of comorbidities among patients with tuberculosis. A more comprehensive gender-responsive approach for patients with tuberculosis and chronic diseases is required to alleviate the double burden of infectious diseases and non-communicable diseases in an aging society.