This paper attempts to present the challenges and issues of inclusion in distance teaching and learning as experienced by Czech university teachers and students during the COVID-19 pandemic. The article offers analytical insights into how the virtual university environment and classrooms were affected by the pandemic crisis. Although several international studies have been conducted on COVID and distance education, only a few have explored in detail the topic of inclusion by covering both the perspectives of university teachers and students. Our results are based on a questionnaire survey of teachers and a pilot questionnaire survey of students administered at a public university in the Czech Republic. Further, the findings highlight the inclusion of students with special needs in the context of the pandemic crisis to provide up-to-date perspectives from university teachers and students on issues related to inclusivity in the teaching and learning environment. The study indicates that more support and further training to teachers are needed regarding issues of inclusion to help bring online learning to the same level as education in brick-and-mortar schools.