Rapid retreat of Arctic sea ice extent in response to global climate warming expends the area of open ocean for new trans-Arctic shipping routes. Ship companies will benefit from the shortened sailing distance across the Arctic, but threats of intensified sea fog induced by the retreated sea ice, especially the potential risk of accidents due to low visibility, are not well considered when designing the trans-Arctic shipping routes. Here, we show that the sailing time along the previous suggested routes will increase nearly 10–30% caused by the impacts of sea fog. We further design a new route detouring to the low-fog-frequency area, based on the projected sea ice extent and the fog frequency in 21st century. The new route is 5–20% longer than the original one, but can save as much as 10% of total sailing time, and most importantly, will lower the risk of catastrophic accidents. Our estimates are similar in both RCP4.5 and 8.5 of CMIP5 simulations.