Although several studies have shown that left-behind adolescents are vulnerable regarding emotional and behavioral functions, much less research has focused on this group’s academic engagement. The relationship between distinct empathy subcomponents and academic engagement in left-behind youth (versus non-left-behind youth) is therefore largely unknown. To fill these knowledge gaps, the current study compared the academic engagement between left-behind and non-left-behind youth. This study subsequently examined the unique and interactive relationships among affective empathy, cognitive empathy, and left-behind status with academic engagement in a combined sample of left-behind and non-left-behind youth. In total, 323 left-behind youth and 737 non-left-behind youth (Mage = 13.05; 49.5% females) participated in this study. Findings, after adjusting for participants’ sociodemographic characteristics, revealed that left-behind youth did not differ significantly in academic engagement compared to non-left-behind youth. A four-step hierarchical regression analysis showed that both empathy components were positively related to academic engagement. Interaction analyses further exhibited a cross-over effect of affective and cognitive empathy for left-behind youth. Specifically, left-behind youth with high cognitive empathy seemed more susceptible to the influence of affective empathy on academic engagement, for better and for worse. In the presence of high affective empathy, left-behind youth with higher cognitive empathy reported the highest academic engagement, whereas the youth with higher cognitive empathy, in the presence of low affective empathy, reported the lowest. The current study highlights the unique and interactive roles of affective and cognitive empathy in left-behind youth’s academic engagement, including important conceptual and practical implications.