This article presents the design and a first pilot evaluation of the computer-based training program Calcularis for children with developmental dyscalculia (DD) or difficulties in learning mathematics. The program has been designed according to insights on the typical and atypical development of mathematical abilities. The learning process is supported through multimodal cues, which encode different properties of numbers. To offer optimal learning conditions, a user model completes the program and allows flexible adaptation to a child’s individual learning and knowledge profile. 32 children with difficulties in learning mathematics completed the 6 to 12-weeks computer training. The children played the game for 20 minutes per day for 5 days a week. The training effects were evaluated using neuropsychological tests. Generally, children benefited significantly from the training regarding number representation and arithmetic operations. Furthermore, children liked to play with the program and reported that the training improved their mathematical abilities.