We study the problem of predicting student knowledge acquisition in online courses from clickstream behavior. Motivated by the proliferation of eLearning lecture delivery, we specifically focus on student in-video activity in lectures videos, which consist of content and in-video quizzes. Our methodology for predicting in-video quiz performance is based on three key ideas we develop. First, we model students' clicking behavior via time-series learning architectures operating on raw event data, rather than defining hand-crafted features as in existing approaches that may lose important information embedded within the click sequences. Second, we develop a self-supervised clickstream pre-training to learn informative representations of clickstream events that can initialize the prediction model effectively. Third, we propose a clustering guided meta-learning-based training that optimizes the prediction model to exploit clusters of frequent patterns in student clickstream sequences. Through experiments on three real-world datasets, we demonstrate that our method obtains substantial improvements over two base-line models in predicting students' in-video quiz performance. Further, we validate the importance of the pre-training and meta-learning components of our framework through ablation studies. Finally, we show how our methodology reveals insights on video-watching behavior associated with knowledge acquisition for useful learning analytics.