Amyloid β (Aβ) aggregation is considered one of the major factors in Alzheimer's disease (AD) pathogenesis. Seeking therapeutic molecules that could inhibit the aggregation effectively has been a major research focus in recent years. Chlorogenic acid (CGA) is reported to have an inhibition effect on Aβ aggregation, and its effectiveness is reported to be enhanced when loaded with selenium nanoparticles. Herein, a previously reported kinetic model based on radical polymerization studying only Aβ aggregation is modified. The modified model is used to study the inhibitory effects of CGA and CGA loaded on nanoparticles on Aβ aggregation. Parameter tuning is done with the experimental data to estimate the values of new parameters introduced in the modified model. The simulated results from the modified model are in good agreement with the experimental data at different doses of both CGA and CGA loaded on the nanoparticles. Moreover, the sensitivity analyses demonstrate the robustness of the model. It is hypothesized that the modified model may help elucidate the Aβ-drug interactions revealing therapeutic insights and may also be used to study the inhibitory effects of other drugs, such as polyphenols, metal chelators, peptides, and nanoparticles that show a similar inhibition trend for the inhibition of Aβ fibrillation.