Providing timely and personalized guidance for students’ programming assignments, particularly by indicating fine-grained error locations with explanations, offers significant practical value for helping students complete assignments and enhance their learning outcomes. In recent years, various automated Fault Localization (FL) techniques, particularly those leveraging Large Language Models (LLMs), have demonstrated promising results in identifying errors in programs. However, existing fault localization techniques face challenges when applied to educational contexts. Most approaches operate at the method-level without explanatory feedback, resulting in granularity too coarse for students who need actionable insights to identify and fix their errors. While some approaches attempt line-level fault localization, they often depend on predicting line numbers directly in numerical form, which is ill-suited to LLMs. To address these challenges, we propose FLAME, a fine-grained, explainable Fault Localization method tailored for programming assignments via LLM-guided Annotation and Model Ensemble. FLAME leverages rich contextual information specific to programming assignments to guide LLMs in identifying faulty code lines. Instead of directly predicting line numbers, we prompt the LLM to annotate faulty code lines with detailed explanations, enhancing both localization accuracy and educational utility. To further improve reliability, we introduce a weighted multi-model voting strategy that aggregates results from multiple LLMs to determine the suspiciousness of each code line. Extensive experimental results demonstrate that FLAME outperforms state-of-the-art fault localization baselines on programming assignments, successfully localizing 207 more faults at top-1 over the best-performing baseline. Beyond educational contexts, FLAME also generalizes effectively to general-purpose software codebases, outperforming all baselines on the Defects4J benchmark.