Jirachi is a pretty hard pokemon to counter all of its sets. As said above, your most surefire counter to Jirachi is Heatran. However, special variants of Jirachi must face this beast.
Meloetta @ Leftovers
Trait: Serene Grace
EVs: 252 HP / 4 Def / 252 SDef
- Perish Song
- Thunder Wave
- Focus Blast
Meloetta's massive special bulk allows it to bypass Jirachi and simply force it out with Perish Song. It also is a handy check to gengar, alakzam, rotom-w, variants of thundurus-t proving it is only a Jirachi Check.
+6 4 SpA Jirachi Flash Cannon vs. 252 HP / 252+ SpD Meloetta: 210-247 (51.98 - 61.13%) -- 94.92% chance to 2HKO
+6 4 SpA Jirachi Psyshock vs. 252 HP / 4 Def Meloetta: 213-251 (52.72 - 62.12%) -- 99.61% chance to 2HKO
Yeah, that's at +6