We report first precision mass measurements of the $1/2^-$ isomeric and $9/2^+$ ground states of $^{101}$In. The determined isomeric excitation energy continues a smooth trend of odd-$A$ indium isotopes up to the immediate vicinity of $N=50$ magic number. This trend can be confirmed by dedicated shell model calculations only if the neutron configuration mixing is considered. We find that the single particle energies are different for different states of the same isotope. The presented configuration-dependent shell evolution, type II shell evolution, in odd-$A$ nuclei is discussed for the first time. Our results will facilitate future studies of single-particle neutron states.