After beating the Elite Four and registering at least 60 Pokemon in your Pokedex to obtain the national upgrade in FR/LG you'll have the chance to run into either Raikou, Entei or Suicune roaming around Kanto depending on the starter you chose.
If you obtained Bulbasaur you'd encounter Entei. If Charmander then you'll see Suicune and if Squirtle, Raikou.
I actually thought it was going to be a real pain to track them down (not to mention catch with no master ball), but it was really easy.
What you need:
- Ultra Balls (or Master ball if you have one)
- Max Repels
- A Pokemon at level 50 or < with a high speed stat (This is the Pokemon you are using to weaken your target)
- A Pokemon with a trapping ability or move (Wobbuffet is recommended)
1. Make your way to Route 6 and make sure you have the Pokemon at level 50 or < you plan to use to weaken your target first in your party.
2. Use a Max Repel and run around in the grass for a little while. If no encounter, enter the building (underground passage) and exit it. (This will reset the location of your legendary).
3. Repeat this process until you encounter it, which usually takes 5 - 10 minutes each encounter). Once you do use your Pokemon to land a hit the legendary will escape. Status moves are recommended. If you have a master ball here, just toss that.
4. Continue to repeat the encounters until you get it's health in the red zone preferably with a status condition.
5. Now switch your lead Pokemon with Wobbuffet or another trapping Pokemon. (It needs to be able to take hits)
6. Encounter it just one more time and start lobbing your Pokeballs at it. You'll catch it eventually.