<p>Extreme wave events pose serious risks to coastal communities, maritime transport and offshore operations, particularly in climatically dynamic regions such as the Indonesian Maritime Continent (IMC). Understanding how large-scale climate modes modulate these extremes is crucial for improving early warning systems and long-term adaptation strategies. This study presents the first long-term, event-based assessment of extreme wave events across the IMC, using 84 years (1940–2023) of ERA5 reanalysis data. Extreme events were identified using the 99th percentile of significant wave height (Hs) and characterized in terms of frequency, duration and intensity at seasonal and annual temporal scales. The results reveal a pronounced north–south seasonal asymmetry driven by the Asian–Australian monsoon: boreal winter extremes dominate the northern IMC (e.g., Natuna Sea) under strong northeasterlies, while boreal summer extremes peak in the southern IMC (e.g., south of Java) under southeasterly trades. Semi-enclosed seas, although less energetic, frequently experience extreme conditions due to lower 99th percentile Hs thresholds and local wind forcing. Focusing on southern Java, the region exhibiting the highest wave severity, the results show that El Niño–Southern Oscillation (ENSO) events do not significantly affect event duration, while El Niño-related combinations tend to supress extreme wave intensity. In contrast, the co-occurrence of La Niña and negative Indian Ocean Dipole (IOD) produces the most intense extremes, associated with enhanced wind stress anomalies. On intraseasonal timescales, active phases of Madden–Julian Oscillation, particularly Phases 2 and 5, strongly modulate extremes waves south of Java during boreal summer, influencing intensity and duration, respectively. These findings highlight the importance of integrating both interannual and intraseasonal climate variability into coastal hazard assessments, maritime operations planning and forecasting systems over the IMC.</p>