Objective To explore the more effective and safer routes of dexmedetomidine administration for sedation in pediatric magnetic resonance imaging (MRI). Methods Eighty children between the age of 1 and 7 years with American Society of Anesthesiologists physical status Ⅰ,Ⅱ scheduled for MRI were divided into two groups according to random number table method (n=40): group V, dexmedetomidine was intravenously pumped at 2 μg/kg for 15 min; group N received intranasal dexmedetomidine 3 μg/kg for 1 min. The heart rate (HR), mean arterial pressure (MAP) , and pulse oxygen saturation (SpO2) of the two groups were recorded before drug administration (T0), 15 min after drug administration (T1), before entering MRI examination room after the children fell asleep (T2), 15 min after entering MRI examination room (T3), at the end of examination (T4), and immediately after awakening (T5). Ramsay Sedation Score at 10, 20 and 30 min after drug administration as well as children′s parent satisfaction were compared between the two groups. Results Compared with T0, the HR of group V decreased at T2, T3 and T4 (P<0.05), and there was no significant difference in HR at different time points in group N (P>0.05). There was no significant difference in MAP and SpO2 between the two groups (P>0.05). Compared with group V, the time for falling asleep and recovery time in group N were longer, and the differences were statistically significant (P<0.05). There was no significant difference in the examination time between the two groups (P>0.05). There was no significant difference in Ramsay Sedation Score between the two groups at 30 min after administration (P>0.05). There was no significant difference in the incidence of adverse events between the two groups (P>0.05), while the parent satisfaction was higher in group N than in group V (P<0.05). Conclusions Intranasal dexmedetomidine 3 μg/kg can offer satisfactory sedation 30 min after administration and have stable hemodynamics, less adverse effects as well as higher parent satisfaction. It is more effective and safer for children undergoing MRI examinations, but the time for falling asleep and recovery time are relatively longer.