Using a variety of visualization tools for teaching and learning science and chemistry is necessary because pupils better understand chemical phenomena and formulate appropriate mental models. The purpose of the presented study was to determine the importance of a virtual laboratory as a visualization element when addressing chemical contents within science classes. Pupils from five different schools who were attending the seventh grade (N = 109), participated in the survey. The pupils were divided into experimental and control groups. We carried out a teaching experiment in order to assess the effectiveness of using a virtual laboratory. In addition, we asked ourselves two questions: whether the dynamic visualization enabled by the use of a virtual laboratory has a positive effect on the learning outcomes of pupils, and how successful are the pupils when solving tasks that involve visualization elements. The results from the didactic experiment showed, that in terms of knowledge acquisition, the use of a virtual laboratory was more effective than classes without the use of dynamic visualization elements.