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Neutron Capture Enhanced Particle Therapy (NCEPT) boosts the effectiveness of particle therapy by capturing thermal neutrons produced by beam-target nuclear interactions in and around the treatment site, using tumour-specific $$^{10}$$ 10 B or $$^{157}$$ 157 Gd-based neutron capture agents. Neutron captures release high-LET secondary particles together with gamma photons with energies of 478 keV or one of several energies up to 7.94 MeV, for $$^{10}$$ 10 B and $$^{157}$$ 157 Gd, respectively. A key requirement for NCEPT’s translation is the development of in vivo dosimetry techniques which can measure both the direct ion dose and the dose due to neutron capture. In this work, we report signatures which can be used to discriminate between photons resulting from neutron capture and those originating from other processes. A Geant4 Monte Carlo simulation study into timing and energy thresholds for discrimination of prompt gamma photons resulting from thermal neutron capture during NCEPT was conducted. Three simulated $$300\times 300\times 300$$ 300 × 300 × 300  mm$$^3$$ 3 cubic PMMA targets were irradiated by $$^4$$ 4 He or $$^{12}$$ 12 C ion beams with a spread out Bragg peak (SOBP) depth range of 60 mm; one target is homogeneous while the others include $$10\times 10\times 10$$ 10 × 10 × 10  mm$$^3$$ 3 neutron capture inserts (NCIs) of pure $$^{10}$$ 10 B or $$^{157}$$ 157 Gd located at the distal edge of the SOBP. The arrival times of photons and neutrons entering a simulated $$50\times 50\times 50$$ 50 × 50 × 50  mm$$^3$$ 3 ideal detector were recorded. A temporal mask of 50–60 ns was found to be optimal for maximising the discrimination of the photons resulting from the neutron capture by boron and gadolinium. A range of candidate detector and thermal neutron shielding materials were simulated, and detections meeting the proposed acceptance criteria (i.e. falling within the target energy window and arriving 60 ns post beam-off) were classified as true or false positives, depending on their origin. The ratio of true/false positives ($$R_{TF}$$ R TF ) was calculated; for targets with $$^{10}$$ 10 B and $$^{157}$$ 157 Gd NCIs, the detector materials which resulted in the highest $$R_{TF}$$ R TF were cadmium-shielded CdTe and boron-shielded LSO, respectively. The optimal irradiation period for both carbon and helium ions was 1 µs for the $$^{10}$$ 10 B NCI and 1 ms for the $$^{157}$$ 157 Gd NCI.