Nowadays, the detection of backscatter X-rays has become an essential part of road security scanners, where individuals are at risk of an accidental exposure to the pulsed photon radiation fields generated by the devices that implement this technique. Dose to soft-tissue measurements of a pulsed radiation field generated by a commercial cargo X-ray backscattering device are presented using a Timepix3 detector. To accurately estimate the imparted dose, the energy spectrum of a backscattering cargo scanner is measured with a thick CdZnTe hybrid semiconductor pixel detector. The deconvolution of this measured spectrum is performed and the contributions to the dose are calculated by means of the mass energy-absorption coefficients for soft-tissue. This methodology was assessed through a Monte-Carlo simulation, together with verification measurements using thermoluminescent detectors (TLDs) as a standard dosimetry system. Measurements of direct irradiation, for a 30 s scan with the device at 2 m from the detector, yielded a dose of (4.9 ± 0.7) μGy and (3.6 ± 0.3) μGy for the Timepix3 and TLDs, respectively. In a simulated cargo environment, with the detector behind a 1 mm thick steel wall, 30 s scan time, and 2 m source to detector distance, the dose measured by the Timepix3 was (1.7 ± 0.1) μGy, while for the TLDs (1.4 ± 0.6) μGy, showing that the proposed methodology has a similar response as compared to a standard dosimetry system.