BackgroundHospital costs for stroke are increasing and variability in care quality creates inefficiencies. In 2007, the Victorian Government (Australia) employed clinical facilitators for three years in eight public hospitals to improve stroke care. Literature on the cost implications of such roles is rare. We report changes in the costs of acute stroke care following implementation of this program.MethodsObservational controlled before-and-after cohort design. Standardised hospital costing data were compared pre-program (financial year 2006–07) and post-program (2010–11) for all admitted episodes of stroke or transient ischaemic attack (TIA) using ICD-10 discharge codes. Costs in Australian dollars (AUD) were adjusted to a common year 2010. Generalised linear regression models were used for adjusted comparisons.ResultsA 20% increase in stroke and TIA episodes was observed: 2624 pre-program (age > 75 years: 53%) and 3142 post-program (age > 75 years: 51%); largely explained by more TIA admissions (up from 785 to 1072). Average length of stay reduced by 22% (pre-program 7.3 days to post-program 5.7 days, p < 0.001). Six hospitals provided cost data. Average per-episode costs decreased by 10% (pre-program AUD7888 to post-program AUD7115). After adjusting for age, sex, stroke type, and hospital, average per-episode costs decreased by 6.1% from pre to post program (p = 0.025). When length of stay was additionally adjusted for, these costs increased by 10.8%, indicating a greater mean cost per day (p < 0.001).ConclusionCost containment of acute inpatient episodes was observed after the implementation of stroke clinical facilitators, likely associated with the shorter lengths of stay.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3836-9) contains supplementary material, which is available to authorized users.