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The interactions of the nucleobases thymine (C5H6N2O2) and uracil (C4H4N2O2) with Cr‐doped C20 fullerene (C19Cr) are investigated by performing density functional theory calculations. The adsorption of these nucleobases on C19Cr leads to two distinct geometries (P1 and P2) differing in the orientation of the nucleobases. The interaction of the nucleobases with the C19Cr nanocluster is highly exothermic, revealing that they are chemically adsorbed on C19Cr. The results show that the binding energy of the thymine–C19Cr complex is slightly higher than that of the uracil–C19Cr complex. In addition, the P2 geometry is more stable compared to P1 due to the higher binding energy in the former configuration. However, based on the results of natural bond orbital and frontier molecular orbitals analyses, the C19Cr nanocage has higher reactivity with the nucleobases in P1 geometry in comparison with P2 due to the larger charge transfer and orbital hybridization in the former geometry. Moreover, the band gap of the C19Cr nanocage decreases after interaction with the nucleobases, and interestingly the impact is more pronounced for P1 geometry, confirming the higher sensitivity of C19Cr to the nucleobases in P1 geometry. Our findings reveal the promising potential of C19Cr as an organometallic carrier for nucleobases thymine and uracil.