Background Children with recurrent infectious diarrhea are susceptible to growth faltering. Docosahexaenoic acid (DHA) and choline may play a role in this relationship due to their involvement in lipid metabolism, gut immunity, and inflammatory pathways. Objectives This study aimed to characterize the contributions made by DHA and choline status and enteric damage in young children in the association between diarrheal illness and child growth. Methods A longitudinal, case-control study was conducted among children ages 6–36 months (N = 195) in Cap-Haitien, Haiti. Mother-child dyads were recruited from community health posts and out-patient clinics. Cases were defined as children experiencing acute diarrhea within the last three days and matched to healthy controls. Child anthropometry, dietary intake, blood, and stool samples were collected at baseline and follow-up. Plasma DHA, choline, and betaine were determined by liquid chromatography-tandem mass spectrometry methods (n = 49) and intestinal fatty acid-binding protein (I-FABP) by enzyme-linked immunoassay (n = 183). Multivariate regression models were applied with mediation analyses to examine associations and adjust for confounding factors. Results At baseline, mean plasma DHA concentrations [1.03 µg/ml (95% CI: 0.91, 1.15)] were not significantly different between cases and controls, nor was there a difference in the mean plasma choline concentrations [4.5 µg/ml (95% CI: 3.8, 5.1)] between groups. Mean plasma I-FABP concentrations were significantly higher at follow-up in cases [3.34 (95% CI: 3.28, 3.40)] vs. controls [3.20 (95% CI: 3.13, 3.27)] (p = 0.002). In adjusted multilinear regression models, higher plasma DHA concentrations at follow-up were associated with a negative change in weight-age-z-score (p = 0.016), and follow-up I-FABP was inversely associated with height-age-z-score (p = 0.035). No interaction or mediation effects were found. Conclusions I-FABP concentrations were significantly higher in cases compared to controls at follow-up, suggesting ongoing enteric damage and increased risk for malnutrition. Plasma DHA and I-FABP may have a role in childhood growth outcomes.