We investigated how the rise rate and decay rate of solar flares affect the thermosphere and ionosphere responses to them. Model simulations and data analysis were conducted for two flares of similar magnitude (X6.2 and X5.4) that had the same location on the solar limb, but the X6.2 flare had longer rise and decay times. Simulated total electron content (TEC) enhancements from the X6.2 and X5.4 flares were ∼6 total electron content units (TECU) and ∼2 TECU, and the simulated neutral density enhancements were ∼15%–20% and ∼5%, respectively, in reasonable agreement with observations. Additional model simulations showed that for idealized flares with the same magnitude and location, the thermosphere and ionosphere responses changed significantly as a function of rise and decay rates. The “Neupert Effect,” which predicts that a faster flare rise rate leads to a larger EUV enhancement during the impulsive phase, caused a larger maximum ion production enhancement. In addition, model simulations showed that increased E × B plasma transport due to conductivity increases during the flares caused a significant equatorial anomaly feature in the electron density enhancement in the F region but a relatively weaker equatorial anomaly feature in TEC enhancement, owing to dominant contributions by photochemical production and loss processes. The latitude dependence of the thermosphere response correlated well with the solar zenith angle effect, whereas the latitude dependence of the ionosphere response was more complex, owing to plasma transport and the winter anomaly.