Radio-iodine refractory (RAI-R) differentiated thyroid cancer (DTC) is a rare disease with a poor prognosis and limited therapeutic resources. Therefore, identifying prognostic factors is essential in order to select patients who could benefit from an early start of treatment. The aim of this study is to identify positron emission tomography with 18F-fluorodeoxyglucose with integrated computed tomography (18F-FDG-PET/CT) parameters to predict overall survival (OS) in patients with RAI-R DTC. In this single-center retrospective study, we analyze the 18F-FDG-PET/CT parameters of 34 patients with RAI-R DTC between April 2007 and December 2019. The parameters collected are MTV, SUVmax and progression for each site of metastasis (neck, mediastinum, lungs, liver, bone) and total sites. ROC curves, Kaplan–Meier survival analysis curves, univariate and multivariate Cox analyses determine prognostic factors for 1-year and 5-year OS. The parameters for mediastinum, liver and total sites are significantly associated with worse 1-year and 5-year OS by both ROC curve analysis and Kaplan–Meier survival analysis. Univariate Cox analysis confirms significance of mediastinum SUVmax (HR 1.08; 95% CI [1.02–1.15]; p = 0.014) and total SUVmax (HR 1.06; 95% CI [1–1.12]; p = 0.042) for worse 1-year OS; of mediastinum SUVmax (HR 1.06; 95% CI [1.02–1.10]; p = 0.003), liver SUVmax (HR 1.04; 95% CI [1.01–1.08]; p = 0.02), liver MTV (HR 2.56; 95% CI [1.13–5.82]; p = 0.025), overall SUVmax (HR 1.05; 95% CI [1.02–1.08]; p = 0.001) and total MTV (HR 1.41; 95% CI [1.07–1.86]; p = 0.016) for worse 5-year OS. Multivariate Cox analysis confirms a significant association between liver MTV (HR 1.02; 95% CI [1–1.04]; p = 0.042) and decrease 1-year OS. In this study, we demonstrate that in RAI-R DTC, 18F-FDG-PET/CT parameters of the mediastinum, liver and overall tumor burden were prognostic factors of poor 1-year and 5-year OS. Identifying these criteria could allow early therapeutic intervention in order to improve patients’ survival.