To report our experience with milk gastroesophageal scintigraphy and the management of gastroesophageal reflux (GER) in children. In 251 pediatric patients we recorded age, underlying disease, central nervous system (CNS) disorders, and GER management. GER management was classified based on treatment plans: grade 0, non-pharmacological treatment; grade 1, non-pharmacological but using a nasogastric tube; grade 2, pharmacological treatment; grade 3, transpyloric feeding; and grade 4, Nissen fundoplication surgery. Patients were included in classified groups with (grades 2, 3, and 4) and without (grades 0 and 1) GER treatment. We evaluated the GER height (classified based on the height of GER, grade 0; no GER, 1; GER in the lower esophagus, 2; GER in the upper esophagus), GER duration in the lower and upper esophagus, presence or absence of massive GER amounts in the lower and upper esophagus, and gastric emptying time. We compared milk scintigraphy results and patient characteristics between groups with (grades 2, 3, and 4) and without (grades 0 and 1) GER treatment. We treated 121 patients for GER. CNS disorders (presence/absence: 46/74 with vs 21/110 without treatment, P < .001). The GER height grade (1.7 ± 0.5 [range, 0–2] with vs 1.5 ± 0.7 [range, 0–2] without treatment, P = .002), massive GER amount (present/absent: 21/99 with vs 9/122 without treatment, P = .011), and duration of GER (seconds) (324.5 ± 508.3 [range, 0–1800] vs 125.0 ± 291.9 [range, 0–1750], P < .001) in the upper esophageal half differed significantly. Similarly massive GER amount (present/absent: 54/66 with vs 34/97 without treatment, P = .002) and GER duration (621.3 ± 601.0 [range, 0–1800] vs 349.8 ± 452.4 [range, 0–1800], P < .001) in the lower esophageal half differed significantly. Additionally, CNS disorders, age, and massive GER in the upper esophageal half differed significantly among grades 2 and 4 in treated patients (P < .05, P < .001, P < .05, respectively). Milk scintigraphy is useful for deciding whether GER treatment is indicated. However, the treatment plan needs to be decided based on each patient’s condition.