Over the years, Waiting for Godot has been subject to a variety of allegorical readings. The most common tend to be philosophical or religious in nature, due to the story's themes regarding the absurd. Both touch on existentialist ideas regarding the meaning of life.

When taken as a philosophical allegory, Godot presents a meaningless universe. Vladimir and Estragon are two men waiting fruitlessly for Godot, a man whose constant absence causes them distress. Godot's identity is never made clear, but that is because it is what he represents that matters, not who he is as a character. Godot gives the men something to wait for—in other words, he gives them meaning. By making Godot absent, Samuel Beckett is suggesting that life is inherently without meaning. Not only that, but life is also absurd, as evidenced by the illogical dialogue and bizarre twists throughout the story. All of this illustrates an absurdist vision of reality.

Godot is often taken as a religious allegory as well. The common observation that the name Godot resembles "God" has led some audiences to assume Godot is meant to be a stand-in for a Judeo-Christian conception of the divine. The two protagonists waiting for Godot are then stand-ins for faithful Christians waiting for God, possibly awaiting the Second Coming of Christ. That Godot never appears suggests that God is distant from humanity or that God does not exist. Others say Godot's absence evokes the loss of religious faith in most Western countries following the devastation of World War Two. It must be noted that Beckett himself rejected such a reading of the play, but many continue to see religious themes anyway.