Background: With the rapid popularization of e-learning, how to improve online learning has aroused widespread concern. A human-like pedagogical agent (PA) that displays eye gaze and gestures, is often added to online multimedia lessons to increase social connection and improve learning in e-learning environments. However, there has been a debate about how PAs affect learning processes and learning outcomes. Objectives: Social agency theory holds that learners can build a social connection with PAs, which affects learning processes and outcomes. This study seeks to reveal how PAs influence learning by exploring the influence of PAs on learning outcomes and brain activity during learning. Methods: College students viewed a multimedia lesson on the process of chemical synaptic transmission either with or without an embodied PA on the left side of the screen that pointed to the graphic as she lectured. During learning students' brain cortical activity was measured by a functional near-infrared spectroscopy (fNIRS) system, and after learning students completed learning outcomes post-tests. Results and Conclusions: Consistent with social agency theory, students learning with a PA performed better on learning outcome tests and showed greater brain activity in the social areas of the brain during learning based on fNIRS measures. Implications: By using fNIRS technology, this study provides preliminary new support for the idea that learners engage in social processing during online learning with an embodied PA that leads to improved learning outcomes.