The purpose of the study was to determine the fluoride (F) and silver (Ag) ions levels in the saliva and urine of healthy children after silver diamine fluoride (SDF) application on dental carious lesions. Sixty children (4-6years with ≥ 3 caries lesions) were recruited from the outpatient department of Pediatric Dentistry. From each child, 3ml unstimulated saliva samples were collected at baseline, one hour, and 24h after SDF application. Similarly, 3ml urine samples were collected prior to and after 24h of SDF application. F and Ag ion concentrations were determined by fluoride ion-selective electrode (ISE) and inductively coupled plasma mass spectrometry (ICPMS), respectively. The mean ± standard deviation (SD) baseline, 1-h, and 24-h salivary F concentrations (ppm) were 0.07 ± 0.07, 0.93 ± 0.48, and 0.19 ± 0.19, respectively, while the mean baseline and 24-h urinary F concentrations (ppm) were 0.33 ± 0.20ppm and 0.43 ± 0.25ppm, respectively. The mean baseline, 1-h, and 24-h salivary Ag concentrations (ppb) were 4.22 ± 3.15, 4198 ± 350, and 56.93 ± 37, respectively. The mean baseline and 24-h urinary Ag concentrations (ppb) were 2.80 ± 2.93ppb and 4.72 ± 4.0ppb, respectively. There were statistically elevated F and Ag ion concentrations at 1h and 24h after SDF application as compared to the baseline. Salivary and urinary F and Ag ions concentrations elevated significantly at 24h following SDF applications in children. A significant high recovery of these ions in urine indicates minimal systemic absorption, thus intermittent topical application of 38% SDF has a minimal risk of toxicity.