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<i>M. avium subsp. paratuberculosis</i> (<i>MAP</i>) is the causative pathogen of Johne&#8217;s disease, a chronic granulomatous enteritis that principally affects ruminants and can survive, proliferate and disseminate in macrophages. MicroRNAs (miRNAs) are important regulators of gene expression and can impact the processes of cells. To investigate the role of miRNAs in monocyte-derived macrophages (MDMs) during <i>MAP</i> infection, we used high-throughput sequencing technology to analyze small RNA libraries of <i>MAP</i>-infected and control MDMs. The results showed that a total of 21 miRNAs were differentially expressed in MDMs after <i>MAP</i> infection, and 8864 target genes were predicted. A functional analysis showed that the target genes were mainly involved in the MAPK signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and apoptosis. In addition, using a dual-luciferase reporter assay, flow cytometry, and a small interfering (si)RNA knockdown assay, the role of miR-150 in regulating macrophage apoptosis by targeting the programmed cell death protein-4 (PDCD4) was demonstrated. These results provide an experimental basis to reveal the regulatory mechanism of MAP infection and suggest the potential of miRNAs as biomarkers for the diagnosis of Johne&#8217;s disease in bovines.