A patient-specific optimisation-based hyperthermia treatment planning program for catheter-based ultrasound technology was developed for a priori evaluation of proposed applicator implant strategies and determination of initial applied power settings. The interstitial and endocavity heating applicators, designed for delivering 3-D controllable hyperthermia within High Dose Rate (HDR) brachytherapy implants, consist of linear and sectored arrays of ultrasound transducers with variable power control in both length and angle. A 3D biothermal model, which incorporates relevant anatomical structures and implant geometries based upon HDR treatment planning, has been developed to simulate the temperature distributions induced by these ultrasound applicators within the catheter implants. A temperature-based constrained optimisation algorithm was devised and integrated within the finite-element thermal solver to determine the optimal applied power levels. A temperature-expressed objective function and constraints were employed to limit maximum temperature (T(max)), maximise target coverage (T(target)), and minimise thermal exposure to normal tissue and surrounding organs. The optimisation-based treatment planning was applied on representative examples of clinical HDR implants for endocavity treatment of cervix (n = 3) and interstitial treatment of prostate (n = 3). Applicator positioning and orientation, T(max), and T(target), were varied, and temperature volume and thermal dose volume histograms calculated for each plan. The optimisation approach provided optimal applied power levels (4-24 independent transducer sections) leading to conforming or tailored temperature distributions for all cases, as indicated with improved temperature index T(90) in the target volume and negligible temperature and thermal dose (t(43,max) < 1 min) exposure in surrounding non-targeted tissues, such as bladder and rectum. The precision of the optimised power estimates was shown to be within <5% for a range of starting levels and were similarly convergent. The execution times of this optimisation (<16 min) and forward thermal treatment planning (<22 min) is sufficiently fast to be integrated into the clinical setting. This optimisation-based treatment planning platform for catheter-based ultrasound applicators is a useful tool to provide feedback for applicator selection (sector angle, number of transducer sections along length), positioning (angle or orientation), optimal initial power settings, and has potential to significantly improve the delivery of hyperthermia in conjunction with HDR brachytherapy.