The treatment of children with inborn errors of metabolism (IEM) is mainly based on restricted dietary intake of protein-containing foods. However, dietary protein restriction may not only reduce amino acid intake, but may be associated with low intake of polyunsaturated fatty acids as well. This review focuses on the consequences of dietary restriction in IEM on the bioavailability of long-chain polyunsaturated fatty acids (LCPUFAs) and on the attempts to ameliorate these consequences. We were able to identify during a literature search 10 observational studies investigating LCPUFA status in patients with IEM and six randomized controlled trials (RCTs) reporting effect of LCPUFA supplementation to the diet of children with IEM. Decreased LCPUFA status, in particular decreased docosahexaenoic acid (DHA) status, has been found in patients suffering from IEM based on the evidence of observational studies. LCPUFA supplementation effectively improves DHA status without detectable adverse reactions. Further research should focus on functional outcomes of LCPUFA supplementation in children with IEM.