Ischemic stroke is a major global disease. Treatment decisions are highly time-sensitive, as eligibility for reperfusion therapies relies on the interval between stroke onset and intervention. However, the true onset time is often uncertain in clinical practice, necessitating imaging-based assessment of tissue age as a surrogate marker. Early ischemic changes on routinely acquired non-contrast CT (NCCT) are often subtle, and real-world clinical datasets exhibit pronounced onset-time class imbalance and center-scanner-related heterogeneity. In this work, we propose StrokeTimer, a fully automated framework for onset-time estimation in acute ischemic stroke. StrokeTimer integrates self-supervised disentanglement learning with energy-guided contrastive learning to capture subtle ischemic patterns while addressing long-tailed data distributions under acquisition variability. Onset time is categorized into three clinically relevant windows: <4.5 h, 4.5-6 h, and >6 h. Experimental results on a large multi-center NCCT dataset from two national cohorts, MR CLEAN Registry and MR CLEAN LATE, show that StrokeTimer achieves a macro AUC of 0.69 and a macro F1-score of 0.57, improving the strongest baseline by nearly 50% (p < 0.005). In this realistic, challenging setting, representative baseline approaches exhibit near-chance macro performance. Model explanations further highlight subtle gray-white matter blurring and hypodense regions consistent with established radiological biomarkers. These findings demonstrate the potential of StrokeTimer to support treatment decision-making in acute ischemic stroke. Code is available at https://github.com/BrainVas/StrokeTimer.