Using Subaru Hyper Suprime-Cam (HSC) year 1 data, we perform the first $k$-cut cosmic shear analysis constraining both $\Lambda$CDM and $f(R)$ Hu-Sawicki modified gravity. To generate the $f(R)$ cosmic shear theory vector, we use the matter power spectrum emulator trained on COLA (COmoving Lagrangian Acceleration) simulations. The $k$-cut method is used to significantly down-weight sensitivity to small scale ($k > 1 \ h {\rm Mpc }^{-1}$) modes in the matter power spectrum where the emulator is less accurate, while simultaneously ensuring our results are robust to baryonic feedback model uncertainty. We have also developed a test to ensure that the effects of poorly modeled small scales are nulled as intended. For $\Lambda$CDM we find $S_8 = \sigma_8 (\Omega_m / 0.3) ^ {0.5} = 0.789 ^{+0.039}_{-0.022}$, while the constraints on the $f(R)$ modified gravity parameters are prior dominated. In the future, the $k$-cut method could be used to constrain a large number of theories of gravity where computational limitations make it infeasible to model the matter power spectrum down to extremely small scales.