Objective The purpose of this study was to examine whether the Insomnia Severity Index (ISI) and Pittsburgh Sleep Quality Index (PSQI) are valid outcome measures for Cognitive Behavioral Therapy for Insomnia (CBT-I). Specifically, we tested whether the factorial parameters of the ISI and the PSQI could remain invariant against CBT-I, which is a prerequisite to using their change scores as an unbiased measure of the treatment outcome of CBT-I. Methods A clinical data set including scores on the Chinese versions of the ISI and the PSQI obtained from 114 insomnia patients prior to and after a 6-week CBT-I program in Taiwan was analyzed. A series of measurement invariance (MI) tests were conducted to compare the factorial parameters of the ISI and the PSQI before and after the CBT-I treatment program. Results Most factorial parameters of the ISI remained invariant after CBT-I. However, the factorial model of the PSQI changed after CBT-I treatment. An extra loading with three residual correlations was added into the factorial model after treatment. Conclusions The partial strong invariance of the ISI supports that it is a valid outcome measure for CBT-I. In contrast, various changes in the factor model of the PSQI indicate that it may not be an appropriate outcome measure for CBT-I. Some possible causes for the changes of the constructs of the PSQI following CBT-I are discussed.