Note taking is a fundamental activity for learning, and many software tools which enable students to take digitized notes have been proposed. Digitized notes are advantageous because they can be easily edited, rearranged, and shared. Although many note-taking tools have been proposed, there has been little research to examine the effect of note annotation and rearrangement with a digitized tool in terms of knowledge acquisition. Therefore, we have investigated the effect of note annotation and rearrangement on how well lecture content is remembered by learners. By annotation, we mean adding both handwritten and typed text, and rearrangement includes moving and deleting handwritten notes. We developed a simple note-taking application specialized for explanation, and evaluated it through a laboratory experiment with eight participants. The results show that note annotation and rearrangement significantly improved how well the participants remembered lecture content. Thus, the effect of annotation and rearrangement on remembrance was confirmed with respect to digitized notes.