The methimazole (MZOL) adsorption by each of representative C24, B12C12, and Al12C12 fullerenes was investigated based on density functional theory (DFT) calculations in an attempt for developing drug delivery systems. The quantum chemical calculations suggested successful formations of MZOL…C24, MZOL…B12C12, and MZOL…Al12C12 complexes. However, the MZOL drug substance was decomposed in the MZOL…C24 system by shifting one hydrogen atom to the fullerene side whereas the original MZOL structure was remained unchanged in the MZOL…B12C12 and MZOL…Al12C12 complexes; the MZOL…B12C12 was the most stable system even in the water and 1-octanol phases. For the formation of complexes, the sulfur atom of MZOL had the significant role in the interactions and a complementary interaction assisted it. By the electronic molecular orbital features, the studied complexes were distinguishable and the role of fullerene was dominant for managing the whole complex system. These results might be used for a fullerene-based nano-carrier drug delivery system.