The extensive distribution of multidrug-resistant (MDR) methicillin-resistant Staphylococcus aureus (MRSA) poses a threat to healthcare worldwide. This study aimed to investigate the MDR and molecular patterns of MRSA isolates in children admitted to the two biggest tertiary care pediatric hospitals in northern and southern Vietnam. A total of 168 MRSA strains were collected to determine antibiotic susceptibility by minimum inhibitory concentration tests. Antibiotic-resistant genes, pulsed-field gel electrophoresis, staphylococcal cassette chromosome mec (SCCmec) typing, and multilocus sequence typing were used for the molecular characterization of MRSA. Among the total strains, the MDR rate (51.8%) was significantly higher in the northern hospital than in the southern hospital (73% vs. 39%, p < 0.0001). The MDR-MRSA with the highest rates were "ciprofloxacin-erythromycin-gentamicintetracyclines" (35.6%), followed by "erythromycin-tetracycline-chloramphenicol" (24.1%), and "ciprofloxacin-erythromycin-gentamicin" (19.5%), showing an accumulative total of 79.3%. The most susceptible antibiotics were rifampicin (100%) and vancomycin (100%), followed by doxycycline (94.0%), meropenem (78.0%), and cefotaxime (75.0%). The SCCmecII strains showed greater resistance to gentamicin, ciprofloxacin, tetracycline, meropenem and cephalosporins compared with the other strains. The SCCmecII strains exhibited the highest rate in the tested genes (aacA/aphD: 55.2%, ermA/B/C: 89.7%, and tetK/M: 82.8%). ST5-SCCmecII was the predominant clone in the northern hospital, whereas SCCmecIVa was more pronounced in the southern hospital. In conclusion, our results raised concerns about the predominant MDR-MRSA strains in the pediatric hospitals in Vietnam. The north-south difference in the antibiotic resistance patterns and genetic structure of MRSA suggests different MRSA origins and various uses of antimicrobial agents between the two regions.