Insomnia disorder (ID) and obstructive sleep apnea (OSA) are the two most prevalent sleep disorders worldwide, but the pathological mechanism has not been fully understood. Functional neuroimaging findings indicated regional abnormal neural activities existed in both diseases, but the results were inconsistent. This meta-analysis aimed to explore concordant regional functional brain changes in ID and OSA, respectively. We conducted a coordinate-based meta-analysis (CBMA) of resting-state functional magnetic resonance imaging (rs-fMRI) studies using the anisotropic effect-size seed-based d mapping (AES-SDM) approach. Studies that applied regional homogeneity (ReHo), amplitude of low-frequency fluctuations (ALFF) or fractional ALFF (fALFF) to analyze regional spontaneous brain activities in ID or OSA were included. Meta-regressions were then applied to investigate potential associations between demographic variables and regional neural activity alterations. Significantly increased brain activities in the left superior temporal gyrus (STG.L) and right superior longitudinal fasciculus (SLF.R), as well as decreased brain activities in several right cerebral hemisphere areas were identified in ID patients. As for OSA patients, more distinct and complicated functional activation alterations were identified. Several neuroimaging alterations were functionally correlated with mean age, duration or illness severity in two patients groups revealed by meta-regressions. These functionally altered areas could be served as potential targets for non-invasive brain stimulation methods. This present meta-analysis distinguished distinct brain function changes in ID and OSA, improving our knowledge of the neuropathological mechanism of these two most common sleep disturbances, and also provided potential orientations for future clinical applications. Registration number: CRD42022301938.