Effect of gravitational magnification on the measurement of distance modulus of type Ia supernovae is presented . We investigate a correlation between magnification and Hubble residual to explore how the magnification affects the estimation of cosmological parameters . We estimate magnification of type Ia supernovae in two distinct methods : one is based on convergence mass reconstruction under the weak lensing limit and the other is based on the direct measurement from galaxies distribution . Both magnification measurements are measured from Subaru Hyper Suprime-Cam survey catalogue . For both measurements , we find no significant correlation between Hubble residual and magnification . Furthermore , we correct for the apparent supernovae fluxes obtained by Supernova Legacy Survey 3-year sample using direct measurement of the magnification . We find \Omega _ { m 0 } = 0.287 ^ { +0.104 } _ { -0.085 } and w = -1.161 ^ { +0.595 } _ { -0.358 } for supernovae samples corrected for lensing magnification when we use photometric redshift catalogue of Mizuki , while \Omega _ { m 0 } = 0.253 ^ { +0.113 } _ { -0.087 } and w = -1.078 ^ { +0.498 } _ { -0.297 } for DEmP photo-z catalogue . Therefore , we conclude that the effect of magnification on the supernova cosmology is negligibly small for the current surveys ; however , it has to be considered for the future supernova survey like LSST .