N osema ceranae is a widespread fungal pathogen of honeybees, which is infective to all castes in the colony, including queens, drones and workers. Nosemosis caused by N. ceranae poses a big challenge for apiculture all over the world. In this articleHere, midguts of normal and N. ceranae-infected Apis cerana cerana workers at 7 (10) days post infection (dpi) were sequenced utilizing small RNA sequencing (sRNA-seq). Totally, 150.54 Mb raw reads were produced in this article, and 144.26 Mb high-quality clean reads with a mean ratio of 95.83% were obtained after strict filtering and quality control. For more insight please see “Comparative identification of microRNAs in Apis cerana cerana workers' midguts responding to Nosema ceranae invasion” [1]. Raw data are available in NCBI Sequence Read Archive (SRA) database under the BioProject number PRJNA487111. Our data can be used for investigating differentially expressed microRNAs (miRNAs) and piRNAs and their regulatory roles engaged in A. c. cerana response to N. ceranae infection, and for offering potential candidates for uncovering the molecular mechanisms regulating eastern honeybee-microsporidian interactions.