We study the ADHM construction of instantons in N = 2 supersymmetric Yang-Mills theory deformed in constant Ramond-Ramond (R-R) 3-form field strength background in type IIB superstrings. We compare the deformed instanton effective action with the effective action of fractional D3/D(-1) branes at the orbifold singularity of C-2/Z(2) in the same R-R background. We find discrepancy between them at the second order in deformation parameters, which comes from the coupling of the translational zero modes of the D(-1)-branes to the R-R background. We improve the deformed action by adding a term with spacetime dependent gauge coupling such that the action reproduces the effective action of the fractional branes.