Insomnia disorder is a prevalent sleep disorder, which affects about 10% of general population. However, its neural mechanisms are poorly understood. Recently, several structural and functional neuroimaging studies have been conducted in patients with insomnia disorder, but these studies have yielded diverse findings. Here, we aimed to identify consistent patterns of abnormal brain alterations in insomnia disorder by performing a quantitative coordinate-based meta-analysis. Following the preferred reporting for systematic reviews and meta-analyses statement, we searched PubMed database and used reference tracking and finally retrieved 19 eligible studies (six task-based functional magnetic resonance imaging, eight resting-state functional magnetic resonance imaging, three voxel-based morphometry, and two positron emission tomography). We extracted peak coordinates from these studies and tested for convergence using the activation likelihood estimation method. Using this method, we found no significant convergent evidence for combination of structural atrophy and functional disturbances across previous studies (p = 0.914). Inconsistencies across these studies might be related to heterogonous clinical populations, the explorative nature of these studies in combination with small sample sizes, different experimental designs, and various preprocessing and statistical approaches. Future neuroimaging studies on insomnia disorder should include larger well-characterized samples, as well as standard imaging and analysis protocols.