The combination of hyperthermia and intravesical chemotherapy is a promising strategy for non-muscle-invasive bladder cancer. However, during intravesical drug administration, the formation of air pockets within the bladder is common and may influence thermal distribution and overall treatment efficacy. Magnetic nanoparticle hyperthermia is a preclinical technique for localized, controllable thermal therapy in bladder cancer. This study numerically investigates the impact of intravesical air pockets on the efficacy of magnetic nanoparticle hyperthermia in stage T1 non-muscle-invasive bladder cancer. A two-dimensional finite element model incorporating the Pennes bioheat equation and Navier–Stokes equations simulated tissue heating and fluid dynamics. Air pockets of two different volumes were analyzed to investigate size-dependent thermal effects, and their positions were varied to examine the influence of direct contact with the tumor compared to no contact. The results showed that air pockets did not alter the magnetic field intensity in the tumor region. Air pockets not in contact with the tumor had no measurable impact on nanoparticle heating or tumor temperature. Air pockets in direct contact with the tumor increased intratumoral temperature, enhanced thermal uniformity, and reduced nanoparticle heating power. Larger tumor-contacting air pockets slightly increased intratumoral temperature without significantly affecting spatial distribution. These findings indicate that air pockets, regardless of size or position, do not compromise the therapeutic effectiveness of magnetic nanoparticle hyperthermia and may offer a procedural advantage over conventional hyperthermia in treating bladder cancer.