Time-course studies of gene expression are essential in biomedical research to understand biological phenomena that evolve in a temporal fashion. We introduce a functional hierarchical model for detecting temporally differentially expressed (TDE) genes between two experimental conditions for cross-sectional designs, where the gene expression profiles are treated as functional data and modeled by basis function expansions. A Monte Carlo EM algorithm was developed for estimating both the gene-specific parameters and the hyperparameters in the second level of modeling. We use a direct posterior probability approach to bound the rate of false discovery at a pre-specified level and evaluate the methods by simulations and application to microarray time-course gene expression data on Caenorhabditis elegans developmental processes. Simulation results suggested that the procedure performs better than the two-way ANOVA in identifying TDE genes, resulting in both higher sensitivity and specificity. Genes identified from the C. elegans developmental data set show clear patterns of changes between the two experimental conditions.