Background Rheumatic heart disease (RHD) is a chronic cardiovascular condition stemming from an infectious origin, posing a substantial health burden, particularly in economically disadvantaged regions. It starts with acute rheumatic fever (ARF), a complication following group A Streptococcus infection, leading to heart valve damage and, over time, structural heart abnormalities. RHD contributes to premature deaths, especially in low-middle-income countries. Although the incidence and prevalence have generally reduced globally due to antibiotics and improved healthcare, it remains a significant public health concern in Brazil, echoing its prevalence in many developing nations around the world. RHD stands as a poignant testament to the intersection of socio-economic disparities and healthcare challenges within Brazil's diverse population. In Brazil, despite advancements in healthcare, RHD continues to impact communities, highlighting the urgent need for enhanced prevention strategies, access to quality healthcare services, and heightened awareness to combat this preventable, yet persistent, cardiac condition. Understanding the epidemiological landscape and socio-cultural factors influencing RHD in Brazil is crucial for developing targeted interventions aimed at mitigating its burden on individuals, families, and the healthcare system at large. Thus, our study focuses on analyzing age-related mortality rates linked to ARF and chronic RHD (ARHD) in Brazil from 2000 to 2021, particularly examining gender disparities. Materials and methods This retrospective cohort study employed a descriptive time-series approach, utilizing comprehensive nationwide data from Brazil spanning from 2000 to 2021 to assess trends in diverse age groups, among both sexes, enabling a detailed analysis of temporal patterns. Mortality data, extracted and categorized meticulously, were subjected to Joinpoint statistical analyses enabling comparative assessments, with average annual percent change (AAPC) and annual percent change (APC) serving as key metrics to quantify and interpret trends over the analyzed period. Results The acute RHD (ARHD)-related mortality declined over the analyzed years supported by AAPC, with higher mortality reduction in females. The age-adjusted mortality rate for "males and females" decreased from 78 to 67 deaths/100,000 from 2000 to 2021. Female mortality dropped from 85 to 69/100,000, and male mortality decreased from 73 to 63/100,000 over the same period. For ARHD, male age groups (20-29, 60-69, 70-79, 80+) showed declining mortality, while the 30-59 age group exhibited an upward. Females AAMR for chronic RHD (CRHD) decreased across all age groups, with significant reductions in the 80 years and above age group from 2000-2002 (APC: -11.94*) and steadily from 2002 onwards (APC: -1.33). Conclusions Our study revealed an overall decline in mortality rates for both acute and CRHD across both sexes. Females consistently exhibited higher mortality rates and a more pronounced reduction compared to males in both acute and CRHD. In ARHD, males experience the highest mortality in the 50-59 age group, while females have a peak in the 40-49 age group. The 60-69 age group had the highest mortality in CRHD for both sexes. Conversely, the 20-29 age group displayed the lowest mortality in CRHD, and the 80-89 age group had the lowest mortality in ARHD.