The COVID-19 pandemic has affected all aspects of the educational system, including students’ learning styles, which are heavily dependent on self-regulated studying strategies and motivation. The purpose of this study was to discover whether Central European students, in this case the Slovak and Czech students, were able to perform self-regulated learning during online learning under the COVID-19 pandemic to achieve their learning goals and improve academic performance, as well as to propose a few practical recommendations how to develop and maintain students’ self-regulation learning in this new online environment. The methodology was based on a questionnaire survey conducted among 268 students at two Central European universities in February and March 2021. The findings indicate that Central European students seemed to be able to perform their online self-study, especially in regard to personal competencies, meaningfulness and motivation. They reported higher awareness of their strengths and weaknesses in learning, time management, and/or the usefulness of making an effort to study. However, the findings reveal an urgent need for more work to be done in the area of metacognitive strategies, such as reflective and critical thinking, analyzing and evaluating. In this respect, the teacher’s role is replaceable since s/he serves as a facilitator and promotes these metacognitive strategies by providing students with constructive feedback, monitoring their learning, reviewing their progress, and/or providing opportunities to reflect on their learning. There were not any striking differences between the Czech and Slovak students. Nevertheless, Slovak students (females in particular) seemed to be more self-disciplined and goal-oriented in their learning.