Cherenkov radiation is generated in optical systems exposed to ionising radiation. In water or plastic devices, if the incident radiation has components with high enough energy (for example, electrons or positrons with energy greater than 175 keV), Cherenkov radiation will be generated. A scintillator dosimeter that collects optical light, guided by optical fibre, will have Cherenkov radiation generated throughout the length of fibre exposed to the radiation field and compromise the signal. We present a novel algorithm to separate Cherenkov radiation signal that requires only a single probe, provided the radiation source is pulsed, such as a linear accelerator in external beam radiation therapy. We use a slow scintillator (BC-444) that, in a constant beam of radiation, reaches peak light output after 1 microsecond, while the Cherenkov signal is detected nearly instantly. This allows our algorithm to separate the scintillator signal from the Cherenkov signal. The relative beam profile and depth dose of a linear accelerator 6 MV X-ray field were reconstructed using the algorithm. The optimisation method improved the fit to the ionisation chamber data and improved the reliability of the measurements. The algorithm was able to remove 74% of the Cherenkov light, at the expense of only 1.5% scintillation light. Further characterisation of the Cherenkov radiation signal has the potential to improve the results and allow this method to be used as a simpler optical fibre dosimeter for quality assurance in external beam therapy.