Hey [mention]iTorkell[/mention]
You have to fight the Nikola boss in Unknown Place to be able to have another chance of catching Jirachi.
Go to Saffron/Goldenrod > Take the Train > Select Trainers Valley > Go to Unknown place.
You can see his team here : https://pokemonrevolution.net/forum/viewtopic.php?f=122&t=77153
Also be careful,cooldown is 21 days,prepare yourself.:P
Goodluck.