Large lepton flavor asymmetries at the QCD epoch could generate a pion condensation phase in the early Universe. For large enough tau lepton flavor asymmetries, the speed of sound can exceed the conformal value, leaving a distinctive imprint on the low-frequency gravitational wave (GW) spectrum from causal sources. Beyond probing the formation of a pion condensation phase, the detection or non-detection of this signature in future Pulsar Timing Arrays (PTAs) datasets would provide a novel constraint on lepton asymmetries in the early Universe. We determine the corresponding GW spectrum and its tilt, comparing them with the standard case of vanishing lepton asymmetry. Finally, we discuss the implications for the stochastic GW background reported by PTAs, using the NANOGrav 15-year dataset.