We construct a noncommutative extension of the Loop Quantum Cosmology effective scheme for the flat FLRW model with a free scalar field via a theta deformation. Firstly, a deformation is implemented in the configuration sector, among the holonomy variable and the matter degree of freedom. We show that this type of noncommutativity retains, to some degree, key features of the Loop Quantum Cosmology paradigm for a free field. Secondly, a deformation is implemented in the momentum sector, among the momentum associated with the holonomy variable and the momentum associated with the matter field. We show that in this latter case the scalar field energy density is the same as the one in standard Loop Quantum Cosmology.