There is increasing regulatory pressure for cost containment in neuro-oncology, and rationalization of the observed regional disparities. We investigated the presence of such disparities in New York State and examined the impact of risk adjustment on the magnitude of this variation. We performed a cohort study involving patients with brain tumors (gliomas, metastases, or meningiomas), who underwent craniotomy for resection from 2009 to 2013, and were registered in the Statewide Planning and Research Cooperative System (SPARCS) database. A linear regression model was utilized for risk-adjustment of inpatient charges using socioeconomic factors and comorbidities. Hospitals with fewer than 20 craniotomies were excluded. 13,535 patients underwent treatment, including 5032 (37.2 %) gliomas, 4858 (35.9 %) metastases, and 3645 (26.9 %) meningiomas. Unadjusted median hospitalization charges ranged from $22,954 to $177,398 at the hospital level, and $30,086 to $159,281 at the county level. Despite extensive risk-adjustment we observed persistent disparities with median hospitalization charges ranging from $40,455 to $124,691 at the hospital level, and $53,999 to $94,844 at the county level. Analysis of variance (ANOVA) demonstrated that these disparities were significant at the facility and the county level (P < 0.0001). Increased charges were not associated with shorter LOS (r = 0.10, P = 0.41), or lower rates of death (r = 0.09, P = 0.46), and unfavorable discharge (r = 0.24, P = 0.06). Using a comprehensive all-payer cohort of patients with brain tumors in New York State we identified wide disparities at the hospital and the county level despite comprehensive risk-adjustment. Increased charges were not associated with shorter LOS, or lower rates of death and unfavorable discharge.