Borono-2-18F-fluoro-phenylalanine (18F-BPA) has been used to estimate the therapeutic effects of boron neutron capture therapy (BNCT), while 18F-fluorodeoxyglucose (18F-FDG) is the most commonly used positron emission tomography (PET) radiopharmaceutical in a routine clinical use. The aim of the present study was to evaluate spatial correlation between 18F-BPA and 18F-FDG uptakes using a deformable image registration-based technique.Ten patients with head and neck cancer were recruited from January 2014 to December 2014. All patients underwent whole-body 18F-BPA PET/computed tomography (CT) and 18F-FDG PET/CT within a 2-week period. For each patient, 18F-BPA PET/CT and 18F-FDG PET/CT images were aligned based on a deformable image registration framework. The voxel-by-voxel spatial correlation of standardized uptake value (SUV) within the tumor was analyzed.Our image processing framework achieved accurate and validated registration results for each PET/CT image. In 9/10 patients, the spatial distribution of SUVs between 18F-BPA and 18F-FDG showed a significant, positive correlation in the tumor volume.Deformable image registration-based voxel-wise analysis demonstrated a spatial correlation between 18F-BPA and 18F-FDG uptakes in the head and neck cancer. A tumor sub-volume with a high 18F-FDG uptake may predict high accumulation of 18F-BPA.