The aim of this study was to evaluate and compare the diagnostic accuracy, the inter-rater agreement and raters' certainty of cone beam computed tomography (CBCT) and radiography for the detection of scaphoid fractures. Our hypothesis is that the CBCT has a higher diagnostic accuracy for scaphoid fractures than radiography. We retrospectively analysed patients who underwent both radiography and CBCT examinations within 4 days to rule out a scaphoid fracture over a 2-year period in our institution. 4 blinded radiologists and orthopaedic surgeons independently rated the images regarding the presence of a scaphoid fracture. The reference standard was evaluated by two radiologists in a consensus reading. Inter-rater correlation was evaluated, pooled sensitivity, specificity, positive and negative predictive values were calculated and compared. 102 patients met the inclusion criteria. 52% of them had a scaphoid fracture. The inter-rater correlation was higher in the CBCT compared to radiography (P < 0.001). Sensitivity, specificity, positive and negative predictive values were higher for CBCT than for radiography (P < 0.019). Observers' fracture classifications showed a higher correlation with the reference standard in the CBCT. Observers' certainty for fracture detection and classification were higher in the CBCT. CBCT shows a higher diagnostic accuracy for scaphoid fractures than radiography.