The objective of this experiment was to test the efficacy of a probiotic (Efinol®L) during transportation of marbled hatchetfish, Carnegiella strigata. Wild specimens were captured from a small stream and transported for 24 h in plastic fish boxes with a probiotic (10 mg L−1) and probiotic-free water. The boxes were sampled at 3, 12 and 24 h of transport. At the end of the experiment, the survival rate was close to 100% in both treatments. Dissolved oxygen diminished with time in both treatments, but the probiotic group had significantly higher levels. Conductivity, pH and ammonia increased significantly during the transport, demonstrating higher levels in the probiotic-free group. Fish from both treatments presented very high net Na+ and K+ effluxes after 3 h of transport. At 24 h, net K+ effluxes in fish of the probiotic treatment reached values close to zero and a significantly lower Na+ efflux was observed. Cortisol levels in both treatments at 3 and 12 h were significantly higher than that in control samples. Higher body cortisol levels were observed in the probiotic-free group than that in the probiotic group at 3 and 12 h. The results demonstrate that addition of a probiotic during fish transport improves water quality and leads to fish presenting a lower stress response intensity.