Accurate patient identification is crucial during admissions in healthcare institutions. Mistaken identity can lead to fatal consequences if patients are treated based on someone else’s medical history. Identifying citizens is generally well-regulated, but accurately identifying foreign, unknown, or anonymous patients is more challenging and often lacks sufficient regulation. Our objective is to develop and assess a coding system for patient identifiers, enhancing the precision of associated health records and offering a robust, adaptable method for identifying patients from diverse backgrounds. We investigated the patient identifier system design in the Estonian National Health Information System (ENHIS) during its shift from the HL7 V3 to the HL7 Fast Healthcare Interoperability Resources (FHIR) communication protocols. This transition involved evolving from an Object Identifier (OID) system to a Uniform Resource Locator (URL) system. We devised an Identifier Domain coding system tailored for patient identification that aligns with our goals and generalised this system as a universal patient identification method. The Design Science methodology, a well-established approach in software engineering and information systems, underpins our research. We tested and illustrated our proposed patient identification coding system using examples from the Estonian Patient Register. This newly developed system enables the identification of all patient types. It is user-friendly, semantically clear, backwards compatible with the OID system, expandable, and aligns with FHIR standards. Our findings can assist in creating interoperable patient identifier systems internationally.