Abstract Concerns over fuel inventory and consequently radiation safety in a fusion device necessitates a better understanding of complex plasma–material interactions. Pulsed induced fluorescence is employed to determine the loss probability of atomic hydrogen on graphite and tungsten in a low-pressure radio-frequency discharge with an applied magnetic field. The interaction between the plasma and material surface leads to a two-stage decay in the atomic hydrogen loss rate in the plasma afterglow, from which the loss probability is determined. The loss rates are found to be dependent on the ion flux. An increase in the ion flux from 1.6×1020m−2s−1 to 5.5×1021m−2s−1 leads to an increase in the loss probability by a factor of two for both graphite and tungsten in the near afterglow. The results demonstrate that the plasma operating conditions play an important role in the loss probability of atomic hydrogen at surfaces of fusion-relevant materials.