Our previous study had found that cellular pseudokinase tribbles 3 (TRIB3) facilitates the infection of enterovirus A71 (EV-A71) via upregulating the protein level of EV-A71 receptor scavenger receptor class B member 2 (SCARB2). In the present study, we used metformin, which had been reported to down-regulate TRIB3 expression, to verify the potential of TRIB3 as an antiviral target. Here, we found that metformin can indeed impede the replication of EV-A71 and Coxsackievirus A16 (CVA16) through inhibiting the transcription of TRIB3 to indirectly down-regulate SCARB2 protein levels to block viral infection. Importantly, we also found that metformin can inhibit the replication of EV-A71 and CVA16 in a TRIB3-independent manner. In fact, we found that both metformin and cellular AMP-activated protein kinase (AMPK) agonist AICAR can inhibit the replication of EV-A71 and CVA16 by pharmacologically activating AMPK. Moreover, AMPK phosphorylation specific inhibitor Compound C treatment can reverse the antiviral effect of metformin, indicating that metformin can indeed play an antiviral role through regulating AMPK. More importantly, we confirmed that metformin could effectively protected mice from lethal EV-A71 infection. Metformin treatment decreased the levels of EV-A71 VP1 protein and viral RNA in the infected muscles, and improved muscle pathology. These findings suggest that TRIB3 does have potential as a target for antiviral drugs, and metformin may be a potential agent or supplement against enterovirus infection.