Atrial flutter is a common supraventricular tachycardia that can be treated using radiofrequency catheter ablation, a procedure that is guided by electroanatomical mapping systems. In this paper, we propose an algorithm for incorporating mapping data into computer simulations of atrial electrical activity with the purpose of creating a more accurate map of electrical activation. The algorithm takes as input the extracellular potential values recorded at a number of sites throughout the atria and estimates the activation time for the entire atrial domain. We test the algorithm using synthetic mapping data and an anatomically detailed atrial geometry with an activation pattern typical of atrial flutter. The results show that the algorithm performs well with synthetic mapping data with information from relatively few mapping sites and in the presence of modeling and measurement error.