Objective: The aims of this study were: 1) to estimate the prevalence of multimorbidity in 2013 and 2019 in adults aged 20–59 years; 2) to assess inequalities in the prevalence of multimorbidity in 2013 and 2019 according to educational level. Methods: Data from two cross-sectional surveys from the Brazilian National Health Survey in 2013 and 2019 were used. Multimorbidity was assessed from 14 lifetime self-reported morbidities (except back problems) and defined using the cutoff point of ≥2 diseases. The prevalence of multimorbidity and individual morbidities were described according to gender, age, skin color, and education. For education, crude, and relative inequalities in prevalence of multimorbidity were calculated using the Slope Index of Inequality and the Concentration Index, respectively. Results: The prevalence of multimorbidity increased from 18.7% (95%CI 18.0–19.3) in 2013 to 22.3% (95%CI 21.7–22.9) in 2019, being higher among women and adults between 30–59 years in both periods. Asthma/bronchitis, depression, and back problems were the conditions that increased the most in the study period. Absolute and relative inequalities by education status were observed in the study period, with worse multimorbidity profiles among the less educated. Conclusion: The prevalence of multimorbidity increased between 2013 and 2019. Inequalities in the prevalence of multimorbidity were observed according to educational level.