The purpose of this study is to clarify whether there is a learning effect on brain activity after writing with an ink pen vs. a digital pen. Previous studies have reported the superiority of handwriting to typing in terms of learning performance, but differences between the use of an ink pen vs. a digital pen remain unclear. In the present study, the participants learned to read difficult words by writing with an ink pen vs. a digital pen. After the learning period, electroencephalography (EEG) signals were measured, while the participants underwent a repetition priming paradigm with the use of the learned words. The repetition priming effect of the N400 event-related potential (ERP) was quantified as an index of the learning effect and the effects between pen types were compared. The groups were also subdivided according to whether a digital pen is frequently used (familiar vs. unfamiliar group). The number of writing repetitions for each word within 10 min during the learning activity and the post-learning test scores were not affected by the pen-type or familiarity with a digital pen. However, the repetition priming effect of the N400 was greater for words written with a digital pen in the learning session, as compared with an ink pen, in the familiar group, but not the unfamiliar group. These results suggest that for those familiar with its use, writing with a digital pen may improve learning relative to the use of an ink pen.