Background: Atopic dermatitis (AD) is characterised by epidermal barrier impairment, associated with food allergen (FA) sensitisation and AD severity. However, no clinical guidance has been established for evaluations of food sensitisation (FS) in AD patients. This study investigated how AD severity and epidermal barrier impairment are associated with FS, and factors that can predict FS in children with AD. Methods: This cross-sectional study included 100 children (12–60 months) diagnosed with AD. AD severity was determined using the Scoring Atopic Dermatitis (SCORAD) index. FS was evaluated by measuring serum specific IgE antibodies against 31 FAs using an immunoblotting method. Epidermal barrier impairment was assessed by measuring transepidermal water loss (TEWL) and stratum corneum hydration (SCH) levels. Results: 90% of participants were sensitised to at least one tested FA, with cow’s milk, egg white, beef, almond, egg yolk, and peanut being the most common. Children with moderate-severe AD had lower SCH levels than those with mild AD. Children with AD who were sensitised to > 10 FAs had significantly higher TEWL and lower SCH levels, compared with those sensitised to 1–4 FAs and 5–10 FAs. The SCORAD score and SCH level in lesional skin provided moderately predictive value for sensitisation to FAs in children with AD. Conclusion: FS is common in children with AD and closely associate with AD severity as well as epidermal barrier impairment. Evaluations of FS should be considered for children with moderate to severe AD and/or low SCH levels.