A fundamental problem in the study of learning is that learning-related changes may be confounded by nonspecific time effects. There are several strategies for handling this problem. This problem may be of greater significance in functional magnetic resonance imaging (fMRI) compared to positron emission tomography (PET). Using the general linear model, we describe, compare, and discuss two approaches for separating learning-related from nonspecific time effects. The first approach makes assumptions on the general behavior of nonspecific effects and explicitly models these effects, i.e., nonspecific time effects are incorporated as a linear or nonlinear confounding covariate in the statistical model. The second strategy makes no a priori assumption concerning the form of nonspecific time effects, but implicitly controls for nonspecific effects using an interaction approach, i.e., learning effects are assessed with an interaction contrast. The two approaches depend on specific assumptions and have specific limitations. With certain experimental designs, both approaches may be used and the results compared, lending particular support to effects that are independent of the method used. A third and perhaps better approach that sometimes may be practically unfeasible is to use a completely temporally balanced experimental design. The choice of approach may be of particular importance when learning related effects are studied with fMRI.