Ultrasonographic remission in addition to clinical remission is probably becoming a new target in the treatment of rheumatoid arthritis. The current study aimed to investigate the risk factors of flare in RA patients who achieved both clinical and ultrasonographic remission. RA patients fulfilled both clinical remission and ultrasonographic remissions were retrospectively enrolled in this study. Baseline clinical, laboratory, and ultrasonographic data were collected. Durations of clinical remission before enrollment and medication strategy during follow-up were recorded. Differences between the flare and the non-flare group were analyzed. Risk factors of flare were assessed with univariate and multivariate Cox proportional hazards models. One hundred and twenty-one RA patients were included. Forty-eight patients relapsed during a median follow-up period of 12.3 months. The flare group had higher percentage of females, shorter duration of clinical remission before enrollment, higher baseline ESR and DAS28 (ESR), and lower baseline gray scale score. Univariate Cox regression revealed female, short duration of remission, high DAS28 (ESR), and failure to achieve 2010 ACR/EULAR remission criteria were risk factors of flare. Furthermore, multivariate analysis showed short duration of remission was the only independent risk factor of flare (HR 0.93, 95% CI 0.88-0.98, P = 0.007). One more month in duration of remission led to a reduction in flare of 7.3%. Short duration of remission at baseline could be an independent risk factor of flare in RA patients who achieved both clinical and ultrasonographic remission, which implicates the significance of sustained remission in the prognosis of RA patients.