We propose a scheme to implement single-qubit operations for singlet-triplet qubits located in an isolated double-well potential with fixed inter-site tunneling when superexchange interactions predominate. Arbitrary single-qubit gates can be realized by a sequence composed of two elementary operations which can be switched between different parameter regimes by adjusting slightly the relative energy bias of trapped atoms in each sub-well site. The experimental feasibility of the strategy and the fidelity of basic rotation operations are also analyzed.