With the reduction in price of next generation sequencing technologies, gene expression profiling using RNA-seq has increased the scope of sequencing experiments to include more complex designs, such as designs involving repeated measures. In such designs, RNA samples are extracted from each experimental unit at multiple time points. The read counts that result from RNA sequencing of the samples extracted from the same experimental unit tend to be temporally correlated. Although there are many methods for RNA-seq differential expression analysis, existing methods do not properly account for within-unit correlations that arise in repeated-measures designs. We address this shortcoming by using normalized log-transformed counts and associated precision weights in a general linear model pipeline with continuous autoregressive structure to account for the correlation among observations within each experimental unit. We then utilize parametric bootstrap to conduct differential expression inference. Simulation studies show the advantages of our method over alternatives that do not account for the correlation among observations within experimental units. We provide an R package rmRNAseq implementing our proposed method (function TC_CAR1) at https://cran.r-project.org/web/packages/rmRNAseq/index.html. Reproducible R codes for data analysis and simulation are available at https://github.com/ntyet/rmRNAseq/tree/master/simulation.