To develop and assess a short-duration JPRESS protocol for detection of overlapping metabolite biomarkers and its application to paediatric brain tumours at 3 Tesla. The short-duration protocol (6 min) was optimised and compared for spectral quality to a high-resolution (38 min) JPRESS protocol in a phantom and five healthy volunteers. The 6-min JPRESS was acquired from four paediatric brain tumours and compared with short-TE PRESS. Metabolite identification between the 6- and 38-min protocols was comparable in phantom and volunteer data. For metabolites with Cramer-Rao lower bounds > 50%, interpretation of JPRESS increased confidence in assignment of lactate, myo-Inositol and scyllo-Inositol. JPRESS also showed promise for the detection of glycine and taurine in paediatric brain tumours when compared to short-TE MRS. A 6-min JPRESS protocol is well tolerated in paediatric brain tumour patients. Visual inspection of a 6-min JPRESS spectrum enables identification of a range of metabolite biomarkers of clinical interest.