<b><i>Background:</i></b> Several recent studies have reported egg yolk-associated food protein-induced enterocolitis syndrome (FPIES) in Japan. We previously reported the usefulness of post-emetic thymus and activation-regulated chemokine (TARC) levels for the diagnosis and evaluation of symptom severity in FPIES caused by solid foods including egg yolk. However, there are no studies on the usefulness of TARC as a prognostic biomarker. <b><i>Objective:</i></b> The aim of the study was to evaluate the post-emetic TARC levels, clinical symptoms, and post-index event results of the egg yolk oral food challenge test (OFC), and retrospectively investigate predictive factors of the subsequent OFC result. <b><i>Method:</i></b> This retrospective study included 12 patients with egg yolk FPIES. The following long-term management protocol for egg yolk FPIES was mandatory for study inclusion: Patients visited the emergency department, met the diagnostic criteria of FPIES, and underwent an egg yolk OFC 6–12 months after complete elimination of egg yolk. If the result of the OFC was positive, the patient underwent the OFC every year until it was negative. We analyzed a total of 20 episodes (12 department visits and eight positive OFCs). The blood test data, including post-emetic TARC level and symptom severity, were compared between the next-OFC-positive group and the next-OFC-negative group. In addition, tolerance development over follow-up was analyzed. <b><i>Results:</i></b> The median (range) ages of the next-OFC-positive and negative groups were 11 (6–33) and 10 (7–21) months, respectively. The median (range) serum TARC (pg/mL) level was 5,208 (2,009–8,147) in the next-OFC-positive group, which was significantly higher (<i>p</i> = 0.004) than that in the next-OFC-negative group, which was 1,803 (905–3,754). There were no significant differences in other hematological results. The next-OFC-positive group had greater severity compared to the next-OFC-negative group (<i>p</i> = 0.026). The remission rate was approximately 30% at 24 months and 80% at 36 months. <b><i>Conclusion:</i></b> Post-emetic TARC levels may predict the short-term prognosis of egg yolk FPIES after approximately 1 year and could be useful for the management of egg yolk FPIES.