The measurement of users' perception of functionalities in the use of Serious Games (SGs) along technology implementation phases may lead to effective changes for developing successful user-centered learning tools in the medical field. In the present data article, data about usability functionalities along two cycles of validation of a SG on neurorehabilitation with final users are described. The key principles of usability model used to collect and analyze data and the evaluation tool are presented. The modifications of the SG to improve usability across implementation phases are detailed. The validation of the SG is described in "Engaged in learning neurorehabilitation: development and validation of a serious game with user-centered design" (Savazzi et al., in press) [1]. The data provided in this article will assist researchers working for developing learning technology to optimize their tools in relation to users' needs and expectations.