Recent studies have demonstrated the feasibility of using passive integrated transponder (PIT) tags for tracking crayfish spatiotemporally in streams. PIT tags can be inserted internally for long-term tracking, assuming low tagging mortality, or attached externally for shorter-term tracking until the individual molts. To date, the practical use of internal cephalothorax tagging has been limited to individuals >30 mm carapace length (CL). The efficacy of internal tagging for small-bodied crayfish species or juveniles of large-bodied species remains poorly understood. We conducted studies with the small-bodied Orconectes compressus (Slender Crayfish) to assess whether internal placement of small PIT tags (8.5 mm long, 2.12 mm diameter) was a viable methodology for future ecological work. In the field, we tagged 63 crayfish and monitored them with a portable transceiver system for 1.5 weeks. In the laboratory, we tagged 21 crayfish and maintained 21 control crayfish for 12 weeks. Crayfish averaged 18 mm CL (n = 84). In the field, there was high initial (14 of 63) and delayed (16 of 63) mortality. We also observed initial (3 of 21) and delayed (11 of 21) mortality in the laboratory within the first 10 days. Smaller individuals had higher mortality rates in both studies. We constructed logistic regression models with field (P = 0.005) and laboratory data (P = 0.027) to show the likelihood of tagging mortality as a function of carapace length. Our results suggest that internal PIT tagging could induce undesirably high mortality in crayfish <22 mm CL for most ecological study objectives.