We investigated whether more arterial stiffness changes could be induced by fragmentation of Swiss ball balance, and examined the role exercise order played in the modulation of arterial stiffness when on-ball kneeling and sitting were combined. Twenty-three healthy young adults (23.8 ± 0.3 years) performed 7 trials in a randomized crossover fashion: CON (non-exercise control), K (on-ball kneeling, 5 min), fK (fragmented on-ball kneeling, 2 × 2.5 min), S (on-ball sitting, 5 min), fS (fragmented on-ball sitting, 2 × 2.5 min), SK (5-min sitting before 5-min kneeling) and KS (5-min kneeling before 5-min sitting). Arterial stiffness in Cardio-ankle vascular index (CAVI) was measured at baseline (BL), immediately (0 min), and every 10 min after exercise, and its changes from BL (ΔCAVI) were calculated. Area under curve (AUC) of ΔCAVI was calculated for SK and KS. The results showed that relative to CON, ΔCAVI decreased at 0 min and 10 min in K and fK, and remained decreased at 20 min in fK only. However, ΔCAVI in S and fS increased with time similarly, with no difference relative to CON. Though ΔCAVI decreased at 10 min in SK, it decreased at both 0 min and 10 min in KS, relative to CON. AUC of ΔCAVI was greater in KS than in SK. The study indicated that compared to continuous mode, fragmented kneeling results in more arterial stiffness improvements, while fragmented sitting exerts no additional effects. When kneeling and sitting are combined, kneeling before sitting elicits more arterial stiffness improvements than sitting before kneeling.