Patients with insomnia disorder (ID) usually experience a greater burden of comorbid anxiety symptoms. However, the neural mechanism under the mutual relationship between ID and anxiety remains largely unclear. The meta-analysis aimed to explore the concordance and distinction of regional brain functional activity in patients with ID and those with generalized anxiety disorder (GAD) using coordinate-based activation likelihood estimation approach. Studies using resting-state regional homogeneity, amplitude of low-frequency fluctuations (ALFF), or fractional ALFF in patients with ID or GAD were included by searching multiple databases up to May 24, 2024. Using meta-analytic approach, 21 studies of ID vs. healthy controls (HC) and 16 studies of GAD vs. HC were included to illuminate the common and distinct patterns between the two disorders. Results showed that ID and GAD shared increased brain activities in the left posterior cingulate cortex and left precuneus, as well as decreased brain activity in the left medial prefrontal cortex. Additionally, compared with ID, GAD showed greater increased activities in the left superior frontal gyrus. Our study reveals both common and different activation patterns between ID and GAD, which may provide novel insights for understanding the neural basis of the two disorders and enlighten the possibility of the development of more targeted treatment strategies for ID and GAD.