Abstract Finding the ground-state energy of molecules is an important and challenging computational problem for which quantum computing can potentially find efficient solutions. The variational quantum eigensolver (VQE) is a quantum algorithm that tackles the molecular groundstate problem and is regarded as one of the flagships of quantum computing. Yet, to date, only very small molecules were computed via VQE, due to high noise levels in current quantum devices. Here we present an alternative variational quantum scheme that requires significantly less qubits than VQE. The reduction in the qubit number allows for shallower circuits to be sufficient, rendering the method more resistant to noise. The proposed algorithm, termed variational quantum selected-configuration-interaction (VQ-SCI), is based on: (a) representing the target groundstate as a superposition of Slater determinant configurations, encoded directly upon the quantum computational basis states; and (b) selecting a-priory only the most dominant configurations. This is demonstrated through a set of groundstate calculations of the H2, LiH, BeH2, H2O, NH3 and C2H4 molecules in the sto-3g basis set, performed on IBM quantum devices. We show that the VQ-SCI reaches the full configuration interaction energy within chemical accuracy using the lowest number of qubits reported to date. Moreover, when the SCI matrix is generated ‘on the fly’, the VQ-SCI requires exponentially less memory than classical SCI methods. This offers a potential remedy to a severe memory bottleneck problem in classical SCI calculations. Finally, the proposed scheme is general and can be straightforwardly applied for finding the groundstate of any Hermitian matrix, outside the chemical context.