The characteristic mode method is used to design a miniaturized dual-band dual circularly polarized (CP) implantable antenna operating in ISM bands. The miniaturization and dual-band characteristics are gained by using the slotting method and by inserting a short-circuit probe between the radiation patch and the ground plane. We use the characteristic mode method to study the current distribution of circular radiation patches with T-shaped slots in different modes. After opening a cross-shaped slot at the center of the radiation patch and the ground plane, we obtained two orthogonal modes with equal amplitude and phase difference of 90° in two operating frequency bands, ultimately achieving CP characteristics of the antenna. Its overall size is only $$\pi$$
π
×(0.014 $$\uplambda$$
λ
0)2 × 0.0027 $$\uplambda$$
λ
0, smaller than other CP implantable antennas with similar performances, and it has satisfactory radiation efficiency and gain characteristics. Measurements show that it can operate in the ISM bands of 0.9 and 2.4 GHz with an effective 3 dB axial ratio bandwidth greater than 220 MHz (0.87 to 1.09 GHz, 22.45%) and 230 MHz (2.31 to 2.54 GHz, 9.48%), and its peak gain is − 29.5 dBi and − 19.2 dBi, respectively. And, this design complies with IEEE safety guidelines.