Functional linear regression has gained popularity as a statistical tool for studying the relationship between function-valued variables. However, in practice, it is hard to expect that the explanatory variables of interest are strictly exogenous, due to, for example, the presence of omitted variables and measurement error. This issue of endogeneity remains insufficiently explored, in spite of its empirical importance. To fill this gap, this article proposes new consistent FPCA-based instrumental variable estimators and develops their asymptotic properties in detail. Simulation experiments under a wide range of settings show that the proposed estimators perform considerably well. We apply our methodology to estimate the impact of immigration on native labor market outcomes in the US.