Cognitive behavioral therapy (CBT) has been shown to be an efficacious treatment for youth anxiety, but we need to know more about the process of change. Affective network variability, or the “spread” of positive and negative emotions activated across a given time period, has been found to be positively associated with anxiety disorder symptomatology, but it is not yet known how this construct changes in response to intervention or its association with anxiety-focused treatment outcomes. The present study used a dynamical systems framework to model ecological momentary assessment (EMA) data collected via a cellular telephone from 114 youth aged 9–14 years (Mage = 10.94, SD = 1.46) who were seeking treatment for a primary anxiety disorder. We examined patterns of affective network variability over time and across (a) CBT and (b) client-centered therapy (CCT) to determine whether affective network changes were specific to CBT or due to nonspecific factors. Associations between treatment outcomes and patterns of affect at pretreatment and over the course of the treatments were also examined. Results revealed significant decreases in affective network variability over the course of treatment for youth who received CBT, but not for youth who received CCT. Changes in affective network variability over the course of treatment did not predict treatment outcomes. Findings provide initial support for the dynamical systems approach to examining changes that occur during treatment. Implications and future research are discussed.