Answers Service 7

Q: What should I say to my son who just announced that he doesn't believe in God and wonders why he should have a Bar Mitzvah?

A: Even atheists can have B Mitzvahs. Here’s why: Though Orthodox rabbis and many Conservative rabbis disagree, a number of Reconstructionist and Humanistic rabbis say you don’t have to believe in God to celebrate Judaism’s beliefs, values and teachings and that atheists can most certainly be good Jews.
Celebrating your B Mitzvah isn’t necessarily the same as proclaiming your belief in God. It’s a ceremony honoring your growing into the age where you are considered a son (or daughter) of the Commandment. You’re acknowledging your desire to participate in Jewish life and that you agree with its values.
More reasons to encourage your 13-year-old atheist to have a B Mitzvah: he may regret it later, should he revise his thinking; and not infrequently, the very process of studying the prayers or reading from an ancient Torah can lead to a change in thinking. We’ve seen children unexpectedly develop a sense of spirituality and get a taste for the profound just by studying with their cantor and rabbi.

Here's an amusingly written account of one young athiest's B Mitzvah.