A substantial loss in the 12q24.23q24.31 area has been associated with neurodevelopmental abnormalities, intellectual difficulties, and developmental delays. There are several chromosomal deletion syndromes worldwide, each with its own set of features. However, the rarity of this deletion in 12q24.23q24.31 presents an opportunity to expand the existing knowledge on this topic. Our case involved a seven-year-old girl with no history of consanguinity, who was discovered to have a 6.6 Mb deletion in the 12q24.23q24.31 region. She was diagnosed with refractory epilepsy, spasticity in all limbs, and global developmental delay with intellectual disabilities. She was able to do basic movements with assistance, identify familiar people, and respond to simple instructions. Some significant physical traits included widely separated eyes, a small nasal tip, and congenital heart defects, such as tricuspid atresia and a single ventricle heart. She also demonstrated clubbing in her fingers and toes, as well as toe overlapping. The purpose of this case report is to contribute to our understanding of deletions in the 12q24.23q24.31 chromosomal region and their clinical implications.