Introduction: in this paper a simulation model for predicting the temperature during the application of focused ultrasound (FUS) for stroke treatment using pulsed ultrasound is presented. Materials and methods: a single element spherically focused transducer of 5 cm diameter, focusing at 10 cm and operating at either 0.5 MHz or 1 MHz was considered. The power field was estimated using the Khokhlov-Zabolotskaya-Kuznetzov (KZK) model. The temperature was estimated using the bioheat equation. The goal was to extract the acoustic parameters (frequency, power, and duty factor) that maintain a temperature increase of less than 1˚C during the application of a pulse ultrasound protocol. Results: it was found that the temperature change increases linearly with duty factor. The higher the power, the lower the duty factor needed to keep the temperature change to the safe limit of 1˚C. The higher the frequency the lower the duty factor needed to keep the temperature change to the safe limit of 1˚C. Finally, the shallow the target, the lower the duty factor needed to keep the temperature change to the safe limit of 1˚C. The simulation model was tested in brain tissue during the application of pulse ultrasound and the measured temperature was in close agreement with the simulated temperature. Conclusions: This simulation model is considered to be very useful tool for providing acoustic parameters (frequency, power, and duty factor) during the application of pulsed ultrasound at various depths in tissue so that a safe temperature is maintained during the treatment. This model will be tested eventually during stroke clinical trials.