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Introduction Early diagnosis and treatment of atrial fibrillation (AF) are crucial to reduce AF-related complications and associated healthcare costs. In low-resource settings, digital health technologies could help achieve this; however, costs of different screening strategies are key for policy change.Methods This decision-tree model representing the Sri Lankan public health system perspective used prevalence data from a community-based cross-sectional study of 10 000 individuals aged ≥50 years in Northern Province, Sri Lanka. Participants were screened for AF using AliveCor, a handheld single-lead ECG device. Three screening strategies (systematic, opportunistic and targeted) were compared against each other. The incremental cost-effectiveness ratio (ICER) is presented, representing the incremental total aggregated cost between screening strategies divided by the incremental number of new detected AF cases to generate a cost per additional new AF cases detected for a 1-year time horizon.Results Systematic screening detected 48 new AF cases, and the targeted screening detected 47. Systematic screening was more expensive (Sri Lankan rupees (Rs) 698 422; US$2123) for 10 000 screened individuals compared with targeted screening (Rs 492 002; US$1496) for 7780 screened individuals. Opportunistic screening was the cheapest strategy (Rs 360 617; US$1096) for screening 6556 individuals; however, only 30 new AF cases were identified. The ICER of targeted screening was lower compared with opportunistic screening (Rs 7729; US$23 per additional detected AF case) whereas the ICER of systematic screening compared with opportunistic screening was higher at Rs 18 767 (US$57) per detected AF case. When the systematic screening strategy was compared with targeted screening, the cost per additional detected AF case increased to Rs 206 420 ($628).Conclusion Targeted screening with AliveCor was the most cost-effective strategy. Systematic screening, while having similar effectiveness, was not cost-effective due to the high additional costs to detect just one further case. These findings support integrating targeted screening into Sri Lanka’s primary care pathways.