Pagels penned The Gnostic Gospels to provide the general public with an insight into a collection of ancient religious texts and to argue that Gnosticism's decline resulted from orthodox Christianity's triumph in establishing a universal, catholic community. She also encourages her readers to use the discovery of the Gnostic texts as a springboard for modern discussions on Christianity, religious authority, humanity, and spirituality. Due to the findings at Nag Hammadi, Pagels states, "all the old questions—the original questions, sharply debated at the beginning of Christianity—are being reopened."

Pagels believes that uncovering and analyzing the Nag Hammadi documents should inspire contemporary men and women to revisit "the controversies that occupied early Christianity." These debates remain as relevant today as they were in the second century, centering on one key question: Where does the church derive its authority? The late discovery of the Nag Hammadi texts in the twentieth century is a fortunate occurrence; had they been found a thousand years earlier, Pagels speculates, they might have been destroyed due to their heretical content. Their discovery today allows many people to read them and reevaluate the theological and philosophical foundations of Gnosticism from a fresh perspective.

Beyond religious matters, the Gnostic texts, according to Pagels, touch on other issues relevant to contemporary life. She contends that psychotherapy shares a notable resemblance to the Gnostic perception of human nature. Both psychotherapy and Gnosticism concur, in contrast to orthodox Christianity, "that the psyche bears within itself the potential for liberation or destruction," as Pagels notes.

Pagels emphasizes that Gnosticism in the second century A.D. was a blend of diverse religious and philosophical ideas. She points out that most Gnostics struggled with the traditional church hierarchy and believed that every member was equally skilled in spirituality. Ideally, in Gnostic gatherings, everyone held the same level of authority. They used a system of drawing lots to determine who would lead a meeting, as they believed that "since God directs everything in the universe, the way the lots fell expressed his choice." In contrast, by the second century, most orthodox Christian communities had a well-established three-tier hierarchy: bishops at the top, followed by priests, and then deacons, with the laity at the bottom of the church's structure.

According to Pagels, when Gnostics drew lots to decide leadership roles during meetings, both men and women participated. While not all Gnostic groups treated women equally, many acknowledged God as "a dyad who embraces both masculine and feminine elements," she explains. She also notes that the Nag Hammadi texts frequently mention a "divine Mother" figure alongside God. However, since Gnostics never unified their beliefs and practices, these depictions of her vary. The divine Mother in these texts is portrayed in three main ways: as the feminine aspect of God, as the Holy Spirit forming an alternate trinity of "Father, Mother, and Son," and as Wisdom, the creator of the universe who also shapes and governs her creations.

Pagels observes that women were notably drawn to Gnostic groups, possibly due to their openness to incorporating the feminine into the divine nature. Several Gnostic groups included women serving equally with men as priests, bishops, prophets, healers, and teachers. In its earliest days, the orthodox Christian church also showed a similar openness to women, she asserts, but after A.D. 200, "we have no evidence for women taking prophetic, priestly, and episcopal roles among orthodox churches."

Pagels writes in a conversational style aimed at general readers rather than scholars. When outlining the book's aims, she uses the first person. For example, in the introduction, she states, "I intend here to show...