Solution doping is a facile approach to fabricating photoactive polymer optical fibers (POFs). However, previous studies reveal that only the cladding of step-index POFs can be doped by the solution doping method in methanol or aqueous solutions, whereas the fiber core is hardly doped. To dope the fiber core as well as the cladding, this study attempts to dope PMMA-based step-index POFs by raising the doping temperatures to near the Tg of PMMA. The results show that a considerable amount of rhodamine B (RhB) is doped in the fiber core, though the amount is still much less than that in the cladding. The highest content in the fiber core is 0.479 mg/g, which is achieved by doping the POFs in water at 110 °C for 8 h. At the same condition, the RhB content of the cladding is 11.5 mg/g. It is found that the high-temperature doping process leads to dramatic axial shrinkage and radial expansion of the POFs, due to the relaxation of the fiber core. The wrinkled cladding after doping suggests that the macromolecule orientation of the core is much higher than that of the cladding, and high orientation should be the main reason why the core is much more difficult to dope than the cladding. Additionally, the doping process at 90 °C in water does not increase the fiber loss regardless of the tremendous POF structure change. In short, the core of PMMA-based step-index POFs can be doped at a temperature near the Tg of the PMMA, making the solution doping technique more practicable for POF doping.