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Abstract Objective Heterozygous variants in KCNQ2 or, more rarely, KCNQ3 genes are responsible for early‐onset developmental/epileptic disorders characterized by heterogeneous clinical presentation and course, genetic transmission, and prognosis. While familial forms mostly include benign epilepsies with seizures starting in the neonatal or early‐infantile period, de novo variants in KCNQ2 or KCNQ3 have been described in sporadic cases of early‐onset encephalopathy (EOEE) with pharmacoresistant seizures, various age‐related pathological EEG patterns, and moderate/severe developmental impairment. All pathogenic variants in KCNQ2 or KCNQ3 occur in heterozygosity. The aim of this work was to report the clinical, molecular, and functional properties of a new KCNQ3 variant found in homozygous configuration in a 9‐year‐old girl with pharmacodependent neonatal‐onset epilepsy and non‐syndromic intellectual disability. Methods Exome sequencing was used for genetic investigation. KCNQ3 transcript and subunit expression in fibroblasts was analyzed with quantitative real‐time PCR and Western blotting or immunofluorescence, respectively. Whole‐cell patch‐clamp electrophysiology was used for functional characterization of mutant subunits. Results A novel single‐base duplication in exon 12 of KCNQ3 (NM_004519.3:c.1599dup) was found in homozygous configuration in the proband born to consanguineous healthy parents; this frameshift variant introduced a premature termination codon (PTC), thus deleting a large part of the C‐terminal region. Mutant KCNQ3 transcript and protein abundance was markedly reduced in primary fibroblasts from the proband, consistent with nonsense‐mediated mRNA decay. The variant fully abolished the ability of KCNQ3 subunits to assemble into functional homomeric or heteromeric channels with KCNQ2 subunits. Significance The present results indicate that a homozygous KCNQ3 loss‐of‐function variant is responsible for a severe phenotype characterized by neonatal‐onset pharmacodependent seizures, with developmental delay and intellectual disability. They also reveal difference in genetic and pathogenetic mechanisms between KCNQ2‐ and KCNQ3‐related epilepsies, a crucial observation for patients affected with EOEE and/or developmental disabilities.