Selenium deficiency is a causative factor in heart failure and microRNAs (known as miRNAs or miRs) play an important role in numerous cardiovascular diseases. However, the changes of miRNA expression during selenium deficiency and whether selenium deficiency is involved in cardiac dysfunction remain unclear. In the present study, miRNA expression profiling was carried out in normal rats, selenium-deficient rats and selenium-supplemented rats by miRNA microarray. Cardiac function was evaluated by analyzing the plasma brain natriuretic peptide level, echocardiographic parameters and hemodynamic parameters. Cardiac glutathione peroxidase activity was assessed by spectrophotometry. The histological changes were examined by hematoxylin and eosin staining. Electrocardiograph was used to test the arrhythmia. The differentially expressed miRNAs were verified by reverse transcription-polymerase chain reaction. Additionally, the underlying mechanism associated with the Wnt/β-catenin signaling pathway was further explored. The cardiac dysfunction of the rat with selenium deficiency was mainly associated with five upregulated miRNAs, which were miR-374, miR-16, miR-199a-5p, miR-195 and miR-30e*, and three downregulated miRNAs, which were miR-3571, miR-675 and miR-450a*. Among these, the expression of miR-374 was the highest, which may be of vital importance in rats with selenium deficiency. In conclusion, the possible mechanism of selenium deficiency-induced cardiac dysfunction was associated with the Wnt/β-catenin signaling pathway.