Foot-and-mouth disease virus (FMDV) is an important disease agent that can be difficult to effectively eradicate from herds. Because it is an obligate intracellular parasite, the virus has multiple effects on the host cell during infection. Here, a high-throughput quantitative proteomic approach was used to develop an unbiased holistic overview of the protein changes in IBRS-2 cells infected with FMDV. Stable isotope labeling with amino acids in cell culture (SILAC) combined with LC-MS/MS was performed to identify and quantify 1260 cellular and 2 viral proteins after 6 h of infection of IBRS-2 cells with FMDV. Of these identified and measured cellular protein pairs, 77 were significantly up-regulated, and 50 were significantly down-regulated based on significance B ≤ 0.05. The differentially altered proteins included a number of proteins involved in endolysosomal proteases system, cell cycle, cellular growth and proliferation, and immune cell trafficking. Selected data were validated by Western blot. Ingenuity Pathway Analysis revealed that proteins that changed in response to infection could be assigned to defined canonical pathways and functional groupings, such as integrin signaling. The obtained data might not only improve the understanding of the dynamics of FMDV and host interaction but may also help elucidate the pathogenic mechanism of FMDV infection.