Prognostic Health Management (PHM) is the disciplined application of measurement, monitoring, and support strategies to protect structural, electrical, or data entities precluding the failure of measured systems in all phases of operation. Model-Based Systems Engineering (MBSE) can be used to formalize system structure, operations, behavior, and requirements using an Architecture Framework (AF), Process Framework (PF), modeling language, and ontology; whereas the AF, PF, and modeling language may be specific to the program or mission employing MBSE, ontologies may be developed specific to a given domain. The PHM domain considers failure modes, effects, and criticality, and ontological system analysis in this domain can inform system structure, operations, behavior, or requirements. A reference ontology for the PHM domain in spacecraft avionics is presented here including aspects of existing ontologies such as the Basic Formal Ontology (BFO), a Top-Level Ontology (TLO) newly recognized by the International Organization for Standardization (ISO), the Information Artifact Ontology (IAO), and the Space Object Ontology (SOO). A distinction is made between a full PHM domain ontology, which would include many mechanical or electrical systems with myriad purposes, and a PHM domain ontology specific to spacecraft avionics. Present ontological development originated using the parlance and format of BFO and IAO in Stanford University’s Protégé software but diverged to include International Union of Pure and Applied Chemistry (IUPAC) terminology and classifications. When interacting with this ontology, engineers seeking to characterize system-specific failure modes, effects, and criticality can query the ontology with their hardware or software entities to obtain failure information specific to the operation of their system in a given operational environment. While this domain ontology is robust, the authors do not claim it to be complete or validated for all spacecraft avionics. It should be considered version one of a useful PHM tool with continual updates occurring after peer review and feedback.