Growth performance is a complex genetic trait that interacts with several environmental variables and life-history attributes, most notably sex and reproduction. Thus, unveiling the genetic architecture of growth remains as a major challenge particularly in flatfish in which sexual dimorphism seems to be a common feature. In this study, we investigated the gene expression profiles and genomic windows associated with growth in the Senegalese sole (Solea senegalensis), which exhibits a female-biased size dimorphism. For this purpose, three fast-growing (FG) and two slow-growing (SG) genetic families were selected according to their breeding values for weight at harvest. Principal component analysis (PCA) using 17 morphometric traits showed that main variation (92.5%) was explained by size and shape. While phenotypic variation clearly separated the FG and SG groups, some differences associated with sex were still observable. Females exhibited greater weight, higher ventral body heights and less elliptical body shapes than males supporting sexual dimorphism both in size and shape. RNA-seq analysis identified 693, 12645 and 1059 differentially expressed transcripts (DETs) between FG and SG in muscle, liver, and brain, respectively. It should be noted a major effect of sex in muscle and liver with 7428 and 15715 DETs, respectively. In these two tissues, >50% of DETs for growth were also co-regulated by sex. Functional analysis using DETs for growth and sex unveiled intricate interactions between vitellogenesis, reproductive status, and growth-related transcriptional networks, particularly in muscle and liver tissues. Main transcriptional enriched pathways associated with growth were closely related to energy provision, cell cycle and signaling. Analysis of sex-specific and growth×sex interacting DETs between males and females highlighted lipid metabolism, macrophagy regulation, cell cycle, DNA and RNA metabolism, ribosome biogenesis, energy provision and maintainance of cellular homeostasis as the most relevant pathways driving sexual dimorphism. A variants analysis using RNA pool-seq data identified eleven genomic windows associated with growth distributed across the genome. Main gene candidates (pptc7, taz, abcd1, tfe3, nfix, ptcd2, prkaa1), whose expression was highly modified by growth, were involved in mitochondrial homeostasis, regulation of mitochondrial activity, energy production and regulation of musculoskeletal system. All these data improve our understanding of the intricate genetic architecture governing growth in sole.