Intake of sugar-sweetened beverages (SSB) may contribute to cardiovascular risk. The aim of this study was to investigate whether functional sugars with low compared to high glycemic index (GI) have beneficial effects on arterial stiffness during a period of low-physical activity. In a controlled cross-over dietary intervention (55% CHO, 30% fat, 15% protein), 13 healthy men (age: 23.7 ± 2.2 years, body mass index: 23.6 ± 1.9 kg/m2) completed 2 × 1 week of low physical activity following 1 week of normal physical activity (2363 ± 900 vs. 11,375 ± 3124 steps/day). During inactive phases participants consumed either low-GI (isomaltulose) or high-GI SSB (maltodextrin-sucrose), providing 20% of energy requirements. Postprandial vasodilatation (augmentation index, AIx), insulin sensitivity (IS) and Glucagon-like-peptide 1 (GLP-1) responses were measured during a meal test before and after SSB-intervention. Compared to maltodextrin-sucrose-SSB, postprandial vasodilatation was prolonged (AIx after 120 min: 9.9% ± 4.3% vs. 11.4% ± 3.7%, p < 0.05) and GLP-1 secretion was higher with isomaltulose-SSB (total area under the GLP-1 curve (tAUCGLP)-1: 8.0 ± 4.4 vs. 5.4 ± 3.4 pM × 3 h; p < 0.05). One week of low-physical activity led to impaired IS that was attenuated with low-GI SSB consumption, but did not affect arterial stiffness (p > 0.05). Higher postprandial GLP-1 secretion after intake of low compared to high-GI beverages may contribute to improved postprandial vasodilatation. Although one week of low-physical activity led to marked impairment in IS, it had no effect on arterial stiffness in healthy men.