The present study aims to test the effectiveness of the Nota Bene (NB) software as an on line annotation tool to enhance students' academic performance and to know their perceptions about the use of this tool. In this research, a quasi-experimental design was used in a private university in Ecuador. The participants were ninety-eight pre-service EFL teachers, who were trained during a five-month period and divided into two groups: control and experimental. They took a pre and a post-test at the beginning and at the end of the training period. The students from the experimental group answered a questionnaire about the perceptions on the use of NB. The statistically significant differences found in the results of the post-test indicate that NB is an effective software to enhance participants' academic performance. In addition, the students who used this tool had positive perceptions about the use of NB while doing their academic activities.