Background: This cross-sectional study aimed to investigate whether a long-term engagement in different types of physical exercise may influence resting-state brain networks differentially. In particular, we studied if there were differences in resting-state functional connectivity measures when comparing older women who are long-term practitioners of tai chi chuan or walking. Method: We recruited 20 older women who regularly practiced tai chi chuan (TCC group), and 22 older women who walked regularly (walking group). Both the TCC group and the walking group underwent a resting-state functional magnetic resonance imaging (rs-fMRI) scan. The acquired rs-fMRI data of all participants were analyzed using independent component analysis. Age and years of education were added as co-variables. Results: There were significant differences in default network, sensory-motor network, and visual network of rs-fMRI between the TCC group and walking group (p < 0.05). Conclusions: The findings of the current study suggested that long-term practice of different types of physical exercises (TCC vs. walking) influenced brain functional networks and brain functional plasticity of elderly women differentially. Our findings encourage further research to investigate whether those differences in resting-state functional connectivity as a function of the type of physical exercise have implications for the prevention of neurological diseases.