A density functional theory method using partially fixed molecular orbitals (PFMOs) is presented. The PFMOs, which have some fixed molecular orbital coefficients and are non-orthogonal, are a generalization of the extreme localized orbitals (ELMOs) of Couty, Bayse, and Hall (1997) Theor Chem Acc 97:96. A non-orthogonal Kohn–Sham method with these PFMOs is derived, and is applied to molecular calculations on the ionization potential of pyridine, the energy difference between cis- and trans-butadiene, the reaction barrier height of the cyclobutene-cis-butadiene interconversion, and the potential energy curve of the hydrogen shift reaction of hydroxycarbene to formaldehyde. The PFMO Kohn–Sham method reproduces well the results of the full Kohn–Sham method without having a restriction on the molecular orbital coefficients. The difference is less than 0.1 eV in the ionization potential and about 0.1 kcal/mol in the barrier height and in the potential energy calculations.