Aim: The goal of this study was to compare the effects of magnetized water and 0.2% chlorhexidine mouthwash on gingivitis and plaque prevention in children aged 12–15 years for a period of 21 days. Materials and methods: A total of 24 youngsters between the ages of 12 and 15 years were chosen. A computer-generated random number sequence was used to split the research participants into two groups. Magnetized water was utilized as a mouthrinse in Category 1, while 0.2% chlorhexidine was employed in Category 2. Water purified with reverse osmosis was stored in glass bottles, which were then put near the magnets to create magnetic water. The magnets had 1000 Gauss power. The bottles were put for a period of 24 hours. The youngsters were given 140 mL of mouthrinse. These mouthrinses were to be used at home, they were told. The Gilmore Turesky adaptation of Quigley Hein's plaque index was used to assess the plaque whereas the gingival index recommended by Loe and Sillness was utilized to assess the gingiva. The plaque index and gingival index were analyzed at baseline, 14 days, and 21 days, as well as history and examination for adverse effects such as bitter taste, brownish discoloration, and so on, were recorded. The trial lasted 21 days with a follow-up period of another 21 days. Results: Both magnetic water and chlorhexidine were similarly successful in managing periodontal and gingival infections; however, magnetized water had less side effects, such as a bitter metallic taste and brown stains. Conclusion: Because of its well-accepted flavor, softer nature, and lower frequency of brown stains, magnetized water can be a safer and more acceptable alternative to chlorhexidine mouthwashes, especially in youngsters. Clinical significance: The use of chlorhexidine as a mouthrinse in the oral cavity has been linked to side effects. These side effects are mostly localized, such as brownish discoloration of teeth, alterations in taste perception, and erosion of the oral mucosa. As chlorhexidine has such negative side effects, it was necessary to do research, particularly in children, to identify a replacement that is similarly efficient against germs but does not have these side effects. Water treated with a magnetic field (magnetized water) was compared with chlorhexidine in the current study.