Strain qualitatively changes the low-energy band structure of bilayer graphene, leading to the appearance of a pair of low-energy Dirac cones near each corner of the Brillouin zone, and a Lifshitz transition (a saddle point in the dispersion relation) at an energy proportional to the strain [ Mucha-Kruczynski, Aleiner and Fal'ko Phys. Rev. B 84 041404 (2011)]. Here, we show that in the vicinity of the Lifshitz transition, the conductance of a ballistic n-p and n-p-n junction exhibits an anomaly: a nonmonotonic temperature and chemical potential dependence, with the size depending on the crystallographic orientation of the principal axis of the strain tensor. This effect is characteristic for junctions between regions of different polarity (n-p and n-p-n junctions), while there is no anomaly in junctions between regions of the same polarity (n-n′ and n-n′-n junctions).