In the Czech Republic, a radical change in the school curriculum is planned. Through a new, compulsory subject of “Informatics and ICT”, the aim is to develop digital literacy across all school subjects, and computational thinking. Computational thinking will be implemented in the curriculum of pre-primary, primary, lower and upper secondary schools, and in teacher education at all faculties of education in the Czech Republic. To ensure readiness for the implementation of the new subject, it has been necessary to prepare and develop a set of learning materials for pupils and teaching guidelines for teachers. These textbooks focus on robotics, programming (Scratch, Python), and theoretical concepts from Informatics. This paper describes a qualitative study aimed at identifying key factors influencing lower secondary pupils’ success in completing some activities related to programming in Scratch. Data were gathered from the feedback of five teachers and 121 pupils at five lower secondary schools, and from the researchers’ observation reports from school visits. The key findings of the study showed that pupils’ success programming in Scratch depends on their motivation to the theme of the Scratch activity, a positive climate in the learning environment, peer collaboration, and freedom in ways to learn new concepts and to find solutions to given problems. Programming in Scratch is promising in developing pupils’ creativity and decision-making in problem-solving. Additionally, a stress-free, non-threatening, learning environment, where the teacher appreciates the enthusiasm, thinking process and effort of pupils to find an original solution has a positive influence on their success.