Long-chain acyl-CoA synthetases (ACSLs) convert long chain fatty acids to acyl-CoAs, the activated substrates essential in various metabolic and signaling pathways. Mutations in ACSL4 are associated with non-syndromic X-linked mental retardation (MRX). However, the developmental functions of ACSL4 and how it is involved in the pathogenesis of MRX remain largely unknown. The Drosophila ACSL-like protein is highly homologous to human ACSL3 and ACSL4, and we designate it as dAcsl. In this study, we demonstrate that dAcsl and ACSL4 are highly conserved in terms of ACSL4's ability to substitute the functions of dAcsl in organismal viability, lipid storage, and the neural wiring in visual center. In neurodevelopment, Decapentaplegic (Dpp, a BMP-like molecule) production diminished specifically in the larval brain of dAcsl mutants. Consistent with the Dpp reduction, the number of glial cells and neurons dramatically decreased and the retinal axons mis-targeted in the visual cortex. All these defects in Drosophila brain were rescued by the wild type ACSL4 but not by the mutant products found in MRX patients. Interestingly, expression of a MRX-associated ACSL4 mutant form in a wild type background led to the lesions in visual center, suggesting a dominant negative effect. These findings validate Drosophila as a model system to reveal the connection between ACSL4 and BMP pathway in neurodevelopment, and to infer the pathogenesis of ACSL4-related MRX.