OBJECTIVES: Incobotulinumtoxin-A is a formulation of botulinum neurotoxin type A (BoNT/A) that is free of complexing proteins. The advantages of incobotulinumtoxin-A include flexible treatment intervals determined by clinical need. The objective of this study was to assess the cost-effectiveness of incobotulinumtoxin-A administered with flexible treatment intervals compared to onabotulinumtoxin-A in blepharospasm (BLEPH) and cervical dystonia (CD) from the Australian healthcare providers’ perspective. METHODS: A Markov state transition model was developed to perform a cost-utility analysis (CUA) comparing the cost and health benefits of incobotulinumtoxin-A with onabotulinumtoxin-A. The CUA compared incobotulinumtoxin-A treatment, given at minimum intervals of 6 weeks and maximum intervals of 20 weeks, with onabotulinumtoxin-A treatment given at fixed 12 week intervals. The Markov model consisted of three health states and followed patients in weekly cycles for one year. Only direct healthcare costs associated with the acquisition and administration of BoNT/A’s were included. Utility values were derived from a prospective, open-labelled cohort study. The primary outcome measure was the incremental cost per quality-adjusted life year (QALY). Univariate and probabilistic sensitivity analyses were conducted. RESULTS: Incobotulinumtoxin-A dominated onabotulinumtoxin-A in both BLEPH and CD. The option to administer incobotulinumtoxin-A according to patient needs resulted in patients experiencing fewer number of weeks with symptoms compared to onabotulinumtoxin-A administered at fixed 12 week intervals. Incobotulinumtoxin-A provided cost savings to the Australian healthcare system. Results held under sensitivity analyses. CONCLUSIONS: Incobotulinumtoxin-A administered at flexible treatment intervals, determined by patient needs, represents a more cost-effective treatment option when compared with onabotulinumtoxin-A in the Australian healthcare system.