Background Childhood cancer survivors are at high risk of developing adverse late health effects. Poor nutritional intake may contribute to this risk, but information about dietary intake is limited. Objective This study will assess childhood cancer survivors’ dietary intake and compare two dietary assessment tools: a self-reported food frequency questionnaire, and dietary measurements from urine spot samples. Methods In a substudy of the Swiss Childhood Cancer Survivor Study (SCCSS), SCCSS-Nutrition, we assessed childhood cancer survivors’ dietary intake via a validated food frequency questionnaire. We sent a urine spot collection kit to a subset of 212 childhood cancer survivors from the French-speaking region of Switzerland to analyze urinary sodium, potassium, urea, urate, creatinine, and phosphate content. We will compare the food frequency questionnaire results with the urine spot analyses to quantify childhood cancer survivors’ intake of various nutrients. We collected data between March 2016 and March 2018. Results We contacted 1599 childhood cancer survivors, of whom 919 (57.47%) returned a food frequency questionnaire. We excluded 11 childhood cancer survivors who were pregnant or were breastfeeding, 35 with missing dietary data, and 71 who had unreliable food frequency questionnaire data, resulting in 802 childhood cancer survivors available for food frequency questionnaire analyses. To a subset of 212 childhood cancer survivors in French-speaking Switzerland we sent a urine spot collection kit, and 111 (52.4%) returned a urine sample. We expect to have the results from analyses of these samples in mid-2019. Conclusions The SCCSS-Nutrition study has collected in-depth dietary data that will allow us to assess dietary intake and quality and compare two dietary assessment tools. This study will contribute to the knowledge of nutrition among childhood cancer survivors and is a step toward surveillance guidelines and targeted nutritional recommendations for childhood cancer survivors in Switzerland. Trial Registration ClinicalTrials.gov NCT03297034; https://clinicaltrials.gov/ct2/show/NCT03297034 International Registered Report Identifier (IRRID) DERR1-10.2196/14427