The gene expression of a cellulase-producing fungus, Acremonium cellulolyticus, was investigated after culturing with three different carbon sources: glycerol, lactose, and Solka-Floc powdered cellulose (SF). High-coverage gene expression profiling (HiCEP) analysis, a method requiring no prior sequence knowledge, was used to screen genes upregulated at the early stage of cellulase production. SF was used as a strong inducer of cellulase production, lactose was used as an inducer of the expression of cellulase genes at the early stage of the culture, and glycerol was used as a negative control. Approximately 15,000 transcript-derived fragments (TDFs) were detected in each sample prepared from the culture grown for 16 h. Based on the expression profiles of the cultured cells, 36 fragments upregulated in both the SF and lactose cultures were selected and sequenced. The deduced gene products of 31 TDFs were likely related to biomass degradation, sugar metabolism, transcriptional regulation, protein modification and metabolism, cell wall recycling, fatty acid and polyketide biosynthesis, and other functions. Quantitative real-time reverse-transcriptase polymerase chain reaction analysis verified that almost all of the transcripts obtained by HiCEP analysis were upregulated in the SF and lactose cultures grown for 18 h. Some of the TDFs in the SF culture were further upregulated over the course of 72 h. The gene products from these TDFs would provide insight into improving the cellulase productivity of A. cellulolyticus.