Neutrino oscillation experiments are known to be sensitive to Non-Standard Interactions (NSIs). We extend the NSI formalism to include one-loop effects. We discuss universal effects induced by corrections to the tree level W exchange, as well as non-universal effects that can arise from scalar charged current interactions. We show how the parameters that can be extracted from the experiments are obtained from various loop amplitudes, which include vertex corrections, wave function renormalizations, mass corrections as well as box diagrams. As an illustrative example, we discuss NSIs at one loop in the Minimal Supersymmetric Standard Model (MSSM) with generic lepton flavor violating sources in the soft sector. We argue that the size of one-loop NSIs can be large enough to be probed in future neutrino oscillation experiments.