Adipose tissue (AT) with a central role in body weight homeostasis, inflammation and insulin resistance, is a highly orchestrated tissue involving receptor and second messenger pathways with steps and passes that influence hyperplasia, hypertrophy, adipocyte differentiation, turnover, lipolysis, free-fatty acid (FFA) metabolism, lipogenesis and the secretome profile. Due to the limitations of the classical molecular biological methods only pieces of the puzzle have been studied, with studies failing to consider the global, time-resolved changes that are evident in this highly plastic organ. “Proteomics”, first coined in 1995 is a large-scale characterization of the entire protein profile of a cell line, tissue, or organism not only from the perspective of expression but also post-translational modifications. As such proteomic technologies offer powerful tools for identifying key components of the adipose proteome, which may contribute to the pathogenesis of adipose tissue dysfunction in obesity. In this review, we plan to address the recent advances in the proteomic characterization of pediatric obesity, in particular the newly identified proteins that potentially play relevant roles and offer targets for novel therapies.