Kammala jumla mai zuwa: Hardee ya yi murabus daga rundunar sojojin Amurka a ranar 31 ga Janairu, 1861, bayan da jiharsa ta Georgia ta rabu da Union. Ya shiga Rundunar Sojojin Tarayyar Amurka a matsayin colonel a ranar 7 ga Maris kuma an ba shi umurnin Fort Morgan da Gaines a Alabama. Daga bisani an daukaka shi zuwa brigadier janar (Yuni 17) da kuma babban janar (Oktoba 7). A ranar 10 ga Oktoba, 1862, ya kasance daya daga cikin manyan jami'an soja na farko. Ayyukansa na farko a matsayin janar shi ne ya shirya brigade na Arkansas regiments kuma ya burge mutanensa da 'yan uwansa ta hanyar warware matsaloli masu wuya da kuma horar da ya ba wa brigade. Ya sami laƙabi, "Tsohon Amintacce", yayin da yake tare da wannan umurnin. Hardee ya yi aiki a Arkansas har sai da aka kira shi ya shiga Janar Albert Sidney Johnston ta Army of Central Kentucky a matsayin kwamandan kwamandan. Johnston zai janye daga Kentucky da Tennessee, zuwa Mississippi, kafin ya kaddamar da harin mamakin a
Yaƙin Shiloh a cikin bazara na 1862. Hardee ya ji rauni a hannun a ranar 6 ga Afrilu, 1862, a ranar farko ta yakin. An kashe Johnston a Shiloh kuma rukunin Hardee ya shiga rundunar Janar Braxton Bragg ta Tennessee kafin kewaye da Corinth, Mississippi, har sai Kwamandan Kwamandan PGT Beauregard ya kwashe garin ya koma Tupelo. An maye gurbin Beauregard da Bragg, wanda daga baya ya tura sojojinsa zuwa Chattanooga kafin ya shiga cikin Confederate Heartland Offensive zuwa Kentucky. Wannan yakin ya ƙare tare da yakin Perryville a watan Oktoba na 1862, inda Hardee ya umurci hagu na hagu na sojojin Bragg.