Objective To investigate the incidence, genetic mutation characteristics, and prognosis of fatty acid oxidation disorder (FAOD) in neonates in Qingdao. Methods Clinical data of neonates diagnosed with FAOD from 2014 to 2023 at the Qingdao Neonatal Disease Screening Center were collected and analyzed to determine the incidence, genotype, and prognosis. Results Among 562 225 neonates screened, 42 were diagnosed with FAOD across six types, yielding an overall incidence of 1/13 386. Primary carnitine deficiency was the most common (20 cases, 48%), with one case showing growth retardation during follow-up. Medium-chain acyl-CoA dehydrogenase deficiency was identified in 6 cases, all of whom demonstrated normal development during follow-up. Short-chain acyl-CoA dehydrogenase deficiency was diagnosed in 5 cases, with one case exhibiting skin erythema, papules, scaling, and dryness during follow-up. Very-long-chain acyl-CoA dehydrogenase deficiency was diagnosed in 5 cases; during follow-up, one patient died and another experienced recurrent rhabdomyolysis. Short/branched-chain acyl-CoA dehydrogenase deficiency was found in 4 cases, with one case showing language regression during follow-up. Multiple acyl-CoA dehydrogenase deficiency was detected in 2 cases; during follow-up, one patient died and one exhibited delayed motor development. Genetic testing performed on 37 of the 42 patients with FAOD identified a hotspot mutation, c.1400C>G, in the SLC22A5 gene among those with primary carnitine deficiency, whereas no predominant hotspot mutations were detected in other FAOD subtypes. Conclusions In Qingdao, primary carnitine deficiency is the most prevalent subtypes of FAOD in neonates, characterized by the hotspot mutation c.1400C>G in the SLC22A5 gene. Except for very-long-chain acyl-CoA dehydrogenase deficiency and multiple acyl-CoA dehydrogenase deficiency, most children with other FAOD subtypes have a favorable prognosis.