Tomatoes are globally significant crops worldwide. Understanding the molecular mechanisms underlying their growth, development, and stress responses is crucial to enhance crop productivity and resilience. The WUSCHEL-related homeobox (WOX) gene family is implicated in developmental processes and stress responses, yet its regulatory complexity in tomato remains underexplored. This study presents an integrative genome-wide analysis approach to characterize the WOX family in tomato. Ten SlWOX genes were identified and phylogenetically classified into three clades, WUS, intermediate and ancient, underscoring their evolutionary relationships. Structural analysis revealed significant variability in gene structure even within the same clade, indicating potential diversity in functional roles. Conserved domains’ screening enables the detection of conserved motifs, including the homeodomain and WUS box. Cis-element analysis showed diverse regulatory elements across the SlWOXs, with a strong emphasis on elements involved in growth and development and stress response. Expression profiling across different organs and growth conditions including abiotic and biotic stresses revealed variability in SlWOXs’ expression patterns. Furthermore, several miRNAs were predicted to target the SlWOXs, emphasizing the existence of post-transcriptional regulation. Functional annotation and interactome analysis further revealed the key role of some SlWOXs, mainly SlWUS, SlWOX4 and SlWOX13, as central regulatory hubs. Collectively, these findings uncover the structural diversity, regulatory mechanisms and functional flexibility of the SlWOX gene family. It also highlights potential targets for improving tomato crop resilience and productivity, making it a significant contribution to plant biology and agriculture.