The statement that information and communication technologies are an essential part of our daily life cannot be contradicted. The digital literacy of the population then influences our entry and opportunities when engaging in the community of peers, in the family, in studies or in the labour market. At the same time, these competences allow us to make decisions, compare information from the media and form our own opinions, or solve personal issues. The urgency of the need for digital competences also provides the scope for reassessment of pedagogical practice, which increasingly requires the inclusion of digital technologies in teaching, not only through curricular documents. The paper presents the content, objectives, methodology and results of the INTERREG-funded project involving teams from the Czech and Slovak Republics. The main objective of the 24-month project (2021–2023) was to create an educational system to improve the skills of teachers and subsequently secondary school pupils. The developed system was based on a virtual classroom environment, LMS and SCORM e-learning reference model. The paper contains partial results of the project in the form of the overall results of the ECDL tests of pupils and their comparison between male and female pupils and between pupils from grammar schools and secondary vocational schools in the Czech Republic. Between the above specified two selected pairs of groups, statistically significant differences were found in the results of individual ECDL test modules focused on various digital competences.