This drug utilization study aimed to investigate prescription patterns and trends for anti-rheumatic drug use in Japanese patients with rheumatoid arthritis (RA), clarifying if patients with RA in Japan are being treated according to EULAR recommendations and ACR guidelines. We used a large-scale claims database consisting of the medical claims of employee health insurance recipients, which included approximately one million insured people. The claims data for incident 5,126 patients with diagnosis codes of RA between January 1, 2005 and October 31, 2011 were analyzed. The number of patients who received disease modifying anti-rheumatic drugs (DMARDs) including biologics as initial therapy was 629 (12.3 %), while the others received non-DMARD therapy only. During the study period, use of methotrexate (MTX) and biologics as first-line drugs increased from 1.9 to 8.0 % and from 0 to 1.6 %, respectively (p < 0.001 for both), while that of non-steroidal anti-inflammatory drugs (NSAIDs) decreased (p = 0.004). Time from first RA diagnosis to the start of treatment with DMARDs decreased significantly from 2005 to 2010. These findings suggest that many early RA patients in Japan do not yet receive aggressive treatment, albeit that this prescribing practice has gradually changed to better comply with clinical recommendations. The current, obsolete Japanese RA guidelines require urgent updating to reflect the most recent knowledge and care with effective treatment modalities.