This paper proposes a new methodology of migration from IEC 61131-3 PLCs to IEC 61499 function blocks. The aim of this migration process is to recreate IEC 61131-3 applications in IEC 61499 implementations with equivalent execution behavior. The formal model of the IEC 61131-3 standard for migration and cyclical execution model is defined. This method also creates a foundation for correct-by-design development tools and automatic migration between the IEC 61131-3 and IEC 61499 standard. Formal migration rules based on ontology mappings, restoring execution model including tasks and programs scheduling and variables mapping with different access levels, are provided. A transformation engine for importing PLC code, mapping from PLC ontology model to function block model and code generation is implemented based on the ontological knowledge base and semantic query-enhanced web rule language. The migration approach is demonstrated on a simple airport baggage handling system.