During launch. The "stack" was actually struck twice, and it caused a major electrical outage in the command module. However, the Saturn V launch vehicle had a completely independent guidance system that was well-protected from electrical discharges, and it continued to function perfectly.

After they got into orbit, the crew and ground controllers got the command module powered up again, did a full system checkout (which showed no damage), and decided to go ahead with the mission. I doubt whether today's NASA would do the same. In fact, it's not at all clear that they made the "prudent" decision then.

Incidentally, this incident caused NASA to change its launch rules in respect to electrical storms; they require much larger distance from the nearest storm now. The reason it happened, which no one had realized until then, is that the plume of ionized gasses from the engines created a low-impedance path from the launch vehicle to ground. In effect, the spacecraft was the tip of the world's tallest lightning rod!