Purpose: In dose painting, functional imaging is used to identify and target radiotherapy‐resistant regions of the tumor. It is important to know if target locations remain stable during radiotherapy, otherwise dose plans will need to adapt to mid‐therapy changes. This study investigated the spatio‐temporal stability of FLT and Cu‐ATSM PET after a few fractions of radiotherapy. Methods: Nineteen canine patients with nasal tumors (12 carcinoma and 7 sarcoma) were imaged prior to accelerated hypofractionated radiotherapy with [F‐18]FLT PET/CT for proliferation and [Cu‐61]Cu‐ATSM PET/CT for hypoxia. FLT scans were repeated after two fractions (8.4 or 10 Gy) and Cu‐ATSM scans after three fractions (12.6 or 15 Gy). Patients were immobilized with custom bite blocks and vacuum mattresses for reproducible positioning. Mid‐treatment scans were rigidly registered to pre‐treatment scans. Spearman correlation coefficients quantified the voxel‐by‐voxel SUV correlations between pre‐ and mid‐treatment scans. Population and histology averaged correlation coefficients were determined using Fisher transformations. SUVmax, SUVmean, SUVpeak, and SUVtotal were also compared between pre‐ and mid‐treatment scans using paired t‐tests. Results: Pre‐ and mid‐treatment scans were highly correlated, for both FLT and Cu‐ATSM PET distributions. The Fisher‐weighted mean Spearman correlation coefficient was 0.87[range: 0.57–0.95] for Cu‐ATSM and 0.79[0.18–0.90] for FLT. On average, sarcomas had slightly higher correlations (0.88) than carcinomas (0.78). We observed significant reductions (p<0.05) in FLT SUVmax, SUVmean, and SUVpeak at mid‐treatment for both histologies. For Cu‐ATSM, carcinomas showed significant reductions in SUVmean, SUVpeak, and SUVtotal, while no significant differences (p>0.20) were observed in sarcomas. Conclusion: Spatial distributions of hypoxia and proliferation were stable after a few fractions of radiotherapy. The magnitude of proliferation reduced significantly in both sarcoma and carcinoma tumors. The magnitude of hypoxia only reduced significantly in carcinoma tumors. With high spatial stability early during radiotherapy, pre‐treatment FLT and Cu‐ATSM PET are potential candidates for dose painting targets.