He held the position of President at Fuller Theological Seminary for 20 years (1993–2013), and continues to hold the post of Professor of Faith and Public Life.

In 2020, Mouw retired from Fuller and returned to Calvin University, becoming a senior research fellow at the Paul B. Henry Institute for the Study of Christianity and Politics.

[5] In 2009, he signed a public statement encouraging all Christians to "read, wrestle with, and respond to Caritas in Veritate", the social encyclical by Pope Benedict XVI.

In November 2004, Mouw offered introductory remarks at a speaking event where Christian evangelist and apologist Ravi Zacharias was the featured speaker, at the Salt Lake Tabernacle at Temple Square in Salt Lake City, Utah.

[11] Multiple Mormon commentators have expressed appreciation for Mouw's efforts to understand their faith to a greater extent.