Misconception is one of the most widely researched topics in science education, including chemical education. This research aims to apply simple graphical visualization tool named Winplot for a learning exercise activity and explore its potency to counter misconceptions about orbitals and quantum numbers. Misconceptions that were countered in this research are the existence of orbitals in atoms and the relationship of magnetic quantum numbers to orbital orientation. This quasi experimental research using pre-test-post-test control group design was conducted to 43 first-year undergraduate students as control class and 45 as experimental class of chemical education at the University of Lampung. The students' pre-existing concepts were analyzed using a pre-test instrument and explored further using in-depth interview. Then, after implementing a learning exercise activity, the conceptual changes were analyzed using a post-test instrument. The results showed that students in experimental class had significant conceptual changes compared to control class. Applying this computer-based strategy is highly recommended to guide students in understanding chemical concepts, especially the topics of orbitals and quantum numbers.