Photodynamic therapy (PDT) outcome depends on the conditions under which it is carried out. Maintaining the tumour tissue oxygen level is important for PDT efficacy and using a low fluence rate can improve outcome. In this work we studied the response of human nasopharyngeal carcinoma tumours in murine models to hypericin-PDT carried out under low fluence and fluence rate. A drug-light interval (DLI) of 1h or 6h was used for 1h-PDT and 6h-PDT, respectively. Evan's blue test was used to assess necrosis and TUNEL staining for apoptosis. Nuclear microscopy was used to quantify elemental concentrations in tumours. Serum vascular endothelial growth factor (VEGF) levels were also determined. TUNEL results showed that 6h-PDT induced significantly more apoptosis compared to 1h-PDT (p<0.01). This was supported by nuclear microscopy showing an increase in calcium and a decrease in zinc levels (both known triggers of apoptosis) in 6h-PDT tumours compared to non-PDT tumours (p<0.05). These results further imply a zinc-mediated pathway in hypericin-PDT induced apoptosis. 6h-PDT also resulted in a significant increase in copper concentrations compared to non-PDT tumours (p<0.05). Serum VEGF levels measured after 6h-PDT were lower than those obtained after 1h-PDT. Overall tumour response to hypericin-PDT under low fluence and fluence rate and using a 6h DLI showed increased apoptosis and lower serum VEGF levels. This treatment regime is suitable for the alternative approach of multi-fraction PDT in which the tumour can be exposed to multiple PDT fractions for complete tumour response. This alternative approach might yield improved outcome.