Most underrated Jirachi counter (and decently anti-meta in general):
Lanturn @ Leftovers
Trait: Volt Absorb
EVs: 52 HP / 252 Def / 204 SDef
Calm Nature (+SDef, -Atk)
- Heal Bell
- Thunder Wave
- Scald / Surf
- Thunderbolt / Volt Switch
Lanturn is a great switch-in to specially-defensive versions, since it takes little to nothing from and Iron Head and can restore Paralysis with Heal Bell, while simultaneously dishing it out with Thunder Wave. Alternatively, you could just spread a burn with Scald or do damage with Surf. What makes Lanturn such a good Jirachi counter, however, is it's typing and ability, Volt Absorb. Calm Mind versions with Thunder/Thunderbolt and Water Pulse/Flash Cannon will struggle to do meaningful damage with their attacks, even boosted:
-4SpAtk
+1 Jirachi (Neutral)
Water Pulse in Rain vs 52HP/200SpDef Leftovers Volt Absorb Lanturn (+SpDef):
10% - 12% (44 - 52 HP).
Guaranteed 10HKO.
-4SpAtk
+1 Jirachi (Neutral)
Flash Cannon vs 52HP/200SpDef Leftovers Volt Absorb Lanturn (+SpDef):
7% - 8% (29 - 34 HP).
Guaranteed 14HKO.
-4SpAtk
+1 Jirachi (Neutral)
Psyshock vs 52HP/252Def Leftovers Volt Absorb Lanturn (Neutral):
35% - 41% (142 - 168 HP).
Guaranteed 3HKO.
Even Psyshock variants struggle, since even at +1, it's only a 3HKO, whereas Lanturn will always break the same Jirachi's sub under rain and can proceed to paralyze and cause major problems.
Also just realized I did my calcs with 200 in SDef rather than 204, but you get the idea.