Evolutionary effects of fishing can have unwanted consequences diminishing a fishery’s value and sustainability. Reserves, or no-take areas, have been proposed as a management tool for reducing fisheries-induced selection, but their effectiveness for migratory species has remained unexplored. Here we develop an eco-genetic model to predict the effects of marine reserves on fisheries-induced evolution under migration. To represent a stock that undergoes an annual migration between feeding and spawning grounds, we draw model parameters from Atlantic cod (Gadus morhua) in the northern part of its range. Our analysis leads to the following conclusions: (i) a reserve in a stock’s feeding grounds, protecting immature and mature fish alike, reduces fisheries-induced evolution, even though protected and unprotected population components mix on the spawning grounds; (ii) in contrast, a reserve in a stock’s spawning grounds, protecting only mature fish, has little mitigating effects on fisheries-induced evolution and can sometimes even exacerbate its magnitude; (iii) evolutionary changes that are already underway may be difficult to reverse with a reserve; (iv) directly after a reserve is created or enlarged, most reserve scenarios result in yield losses; and (v) timescale is very important: short-term yield losses immediately after a reserve’s creation can give way to long-term gains.