AbstractMeasurement error is an important problem that has not been studied very well in the context of functional data analysis. To the best of our knowledge, there are no existing methods that address the presence of functional measurement errors in generalized functional linear models. In this article, a novel approach is proposed to estimate the slope function in the presence of measurement error in the generalized functional linear model with a scalar response. This work significantly advances the existing conditional score method to accommodate the case where both the measurement error and independent variables lie in infinite dimensional spaces. Asymptotic results are established for the proposed estimate, and its behaviour is studied via simulations, where the response is continuous or binary. Analysis of Canadian Weather data highlights the practical utility of our method. The Canadian Journal of Statistics 48: 238–258; 2020 © 2020 Statistical Society of Canada