A deficiency of the enzyme arylsulfatase A (ARSA) causes a progressive neurodegenerative lysosomal storage disease known as metachromatic leukodystrophy (MLD). Diagnosis is based on the onset of neurological symptoms, presence of gait abnormalities, spasticity, decreased muscle stretch reflexes and neuro-radiological evidence of demyelination. The purpose of the present study was to identify any mutation in the candidate ARSA gene in a family of late infantile MLD patients. The diagnosis of suspected MLD patients was confirmed by a MRI report and low ARSA enzymatic activity in leukocytes. Sanger sequencing of full-length coding regions of ARSA gene was performed. Changes in the nucleotide sequence were determined by comparing the obtained data with the wild-type sequence. mRNA expression was analysed using real-time PCR. A novel base pair substitution at position c.338T>C (p.L113P) of ARSA gene was observed in the family and was confirmed in a normal population via ARMS-PCR and Sanger sequencing. The mRNA expression of ARSA gene showed a significant difference between normal and carrier individuals (p = 0.0008). In silico analysis by POLYPHEN, a pathogenicity prediction tool, predicted the possible damaging nature of this mutation. I-TASSER, a protein-modelling server, demonstrated the effects of this mutation on different domains of the ARSA protein, which plays a crucial role in the structural and functional integrity of enzyme. The novel p.L113P mutation in a Pakistani family with late infantile MLD has a pathogenic and destructive effect on the protein structure and function of ARSA. It is the first case reported in a Pakistani population using genetic analysis.