Bifurcating Markov chains (BMCs) are Markov chains indexed by a full binary tree representing the evolution of a trait along a population where each individual has two children. We provide a central limit theorem for additive functionals of BMCs under $L^2$ -ergodic conditions with three different regimes. This completes the pointwise approach developed in a previous work. As an application, we study the elementary case of a symmetric bifurcating autoregressive process, which justifies the nontrivial hypothesis considered on the kernel transition of the BMCs. We illustrate in this example the phase transition observed in the fluctuations.