The authors propose parallel rate-variable punctured convolutional coded PPM (pulse position modulation) in a photon counting channel to achieve high energy information efficiency for desired bit error rate (BER) and transmission bandwidth. They theoretically show the BER performance, the bandwidth expansion factor β, and a necessary energy information efficiency to achieve BER = 10-6 of the proposed systems for some combinations of code rates. It is found that the system with the same code rates on all binary erasure channels has better BER performance than other systems for the same bandwidth expansion factor β. It is also found that the proposed system can achieve high energy information efficiency for desired BER and β by selecting a suitable combination of code rates depending on the channel conditions. Moreover, it is shown that the proposed system has better BER performance than Reed-Solomon-coded PPM in a small range of β.