Objectives To examine the comorbidity burden in patients with rheumatoid arthritis (RA) patients using a nationwide population-based cohort by assessing the Charlson Comorbidity Index (CCI), Elixhauser Comorbidity Index (ECI), Multimorbidity Index (MMI), and Rheumatic Disease Comorbidity Index (RDCI) scores and to investigate their predictive ability for all-cause mortality. Methods We identified 24,767 RA patients diagnosed between 1998–2008 in Taiwan and followed up until December 31, 2013. The incidence of comorbidities was estimated in three periods (before, during, and after the diagnostic period). The incidence rate ratios were calculated by comparing during vs. before and after vs. before the diagnostic period. One- and 5-year mortality rates were calculated and discriminated by low and high-score groups and modified models for each index. Results The mean score at diagnosis is 0.8 in CCI, 2.8 in ECI, 0.7 in MMI, and 1.3 in RDCI, and annual percentage changes are 11.0%, 11.3%, 9.7%, and 6.8%, respectively. The incidence of any increase in the comorbidity index is significantly higher in the periods of ‘during’ and ‘after’ the RA diagnosis (incidence rate ratios for different indexes: 1.33-2.77). The mortality rate significantly differs between the high and low-score groups measured by each index (adjusted hazard ratios: 2.5-4.3 for different indexes). CCI is slightly better in the prediction of 1- and 5-year mortality rates. Conclusion Comorbidities are common before and after RA diagnosis, and the rate of accumulation accelerates after RA diagnosis. All four comorbidity indexes are useful to measure the temporal changes and to predict mortality.