Abstract Background: Allan-Herndon-Dudley syndrome (AHDS) is an X-linked disorder caused by a pathogenic variant in the SLC16A2gene. Although most reported variants are found in protein-coding regions or adjacent junctions, structural variations (SVs) within non-coding regions have not been previously reported. Methods: To investigate two male siblings with severe neurodevelopmental disorders and spasticity, who had remained undiagnosed for over a decade and were negative from exome sequencing, we utilized long-read HiFi genome sequencing. We analyzed short-tandem repeats (STRs) and SVs to identify the genetic cause in this familial case. Results: While coding variants and STR analyses yielded negative results, SV analysis revealed a novel hemizygous deletion in intron 1 of the SLC16A2 gene (ChrX:74,460,691-74,463,566; 2,876 bp), inherited from their carrier mother and shared by the siblings. Determination of the breakpoints indicates that the deletion probably resulted from Alu/Alu-mediated rearrangements between homologous AluY pairs. The deleted region is predicted to include multiple transcription factor binding sites, such as Stat2, Zic1, Zic2, and FOXD3, which are crucial for the neurodevelopmental process, as well as a regulatory element including an eQTL (rs1263181) that is implicated in the tissue-specific regulation of SLC16A2 expression, notably in skeletal muscle and thyroid tissues. Conclusions: This report, to our knowledge, is the first to describe a non-coding deletion associated with AHDS, demonstrating the potential utility of long-read sequencing for undiagnosed patients. It may expand the genomic spectrum of AHDS and highlight the identified region with a high priority for future investigation and functional studies.