Background and Objectives: This prospective, comparative, double-cohort study aimed to compare the efficacy of silver diamine fluoride and potassium iodide (38% SDF+KI; Riva Star®) with sodium fluoride varnish (5% NaF; Duraphat®) in hypersensitive carious lesions in primary teeth to evaluate caries arrest and hypersensitivity relief. Materials and Methods: This study included thirty 2-5-year-olds (mean age = 3.67 ± 1.06 years; 16 males and 14 females) who required a desensitizing treatment for hypersensitive carious defects with visible dentin. A total of 15 of the participants were consecutively allocated to treatment with 5% NaF, and they were further compared to an equal number of participants treated with 38% SDF+KI solutions (n = 15). The treatments were performed following clinical evaluation of caries activity using the International Caries Classification and Management System (ICCMSTM) and the Bjørndal criteria (score of 0-9). Parental-reported hypersensitivity was evaluated using a visual analogue scale (0-10 = no to severe pain). Results: Clinical variables were evaluated at baseline and three months after treatment. Thereafter, a significant decline in hypersensitivity/pain led to lower final scores in the Riva Star® group (0.40 ± 1.12, p = 0.002) than in the Duraphat® group (1.40 ± 2.20, p = 0.004). The caries arrest effect was significantly higher in the Riva Star® group (86.7%) compared to the Duraphat® group three months after treatment (13.3%, p < 0.001). In both groups, there were no statistically significant differences in the children's behavior before, during, and after treatment. Conclusions: Ultimately, with both fluoride therapies reducing hypersensitivity/pain significantly, treatment with 38% SDF+KI was clearly more effective in caries arrest than 5% NaF varnish after a 3-month period.