Gastrointestinal (GI) side effects caused by chemotherapy in women with breast cancer are common but poorly understood which might be controlled by nutritional intervention. Thus, the major aim of this study was to assess the effect of dietary intervention along with nutritional education on reducing these side effects. The present study is a single-center, single-controlled, and randomized trial. A total of 150 patients with breast cancer undergoing chemotherapy were randomly assigned into intervention group to receive dietary intervention and nutritional education (n = 73) or control group (n = 67) for 10 weeks, after their three sessions of chemotherapy. The primary endpoint was the GI symptoms after each session of chemotherapy that were measured by a designed questionnaire based on ROMIII questionnaire. The severity of GI side effects in the dietary intervention along with nutritional education was decreased significantly in the third session of chemotherapy compared to the first session, which include reflux disorder (P = 0.05), anorexia (P < 0.001), nausea (P = 0.002), constipation (P < 0.001), and diarrhea (P < 0.001). Moreover, significant reductions were observed in the severity of GI side effects in the intervention group compared to control group after the third session (P < 0.001). After adjusting the analysis for baseline values including age, job, education level, weight, and body mass index, significant changes were observed for GI side effects in the intervention group compared to the control group (P < 0.001). This study showed beneficial effects of individualized dietary intervention along with nutritional education on reducing diarrhea, constipation, vomiting, and nausea in women with breast cancer during the chemotherapy.