In this paper, we study the buffered clock tree synthesis problem under thermal variations for 3D IC technology. Our major contribution is the Balanced Skew Theorem, which provides a theoretical background to efficiently construct a buffered 3D clock tree that minimizes and balances the skew values under two distinct non-uniform thermal profiles. Our clock tree synthesis algorithm named BURITO (buffered clock tree with thermal optimization) first constructs a 3D abstract tree under the wirelength vs via-congestion tradeoff. This abstract tree is then embedded, buffered, and refined under the given non-uniform thermal profiles so that the temperature-dependent skews are minimized and balanced. Experimental results show that our algorithms significantly reduce and perfectly balance clock skew values with minimal wirelength overhead.