The current study aims to explore the functional changes of the amygdala in patients with euthymic Bipolar Disorder (BD) using resting state fMRI (rs-fMRI). Twenty-one euthymic patients with bipolar disorder and 28 healthy controls participated in this study. Two of the euthymic patients with BD and three of the healthy controls were excluded due to excessive head motion. We found that patients with euthymia (38.79 ± 12.03) show higher fALFF (fractional Amplitude of low-frequency fluctuation) value of the amygdala (t = 2.076, P = 0.044), and lower functional connectivity between the amygdala and supplementary motor area (p < 0.01, GRF corrected) than healthy controls (33.40 ± 8.21). However, euthymic patients did not show a differential activity in ReHo (Regional Homogeneity) and gray matter of the amygdala region as compared to healthy controls. Thus, despite the absence of clinical symptoms in euthymic patients with BD, the amygdala functional activity and its connectivity to other brain regions remain altered. Further investigation of negative emotions and social functioning in euthymic patients with BD are needed and can help pave the way for a better understanding of BD psychopathology.