Kammala jumla mai zuwa: Da yake shiga cikin rundunar Sojojin Tarayya a watan Afrilun 1861, Kennedy ya zama kyaftin na Kamfanin E, 2nd South Carolina Infantry Regiment, a karkashin dan uwansa na Camden Col. Joseph Brevard Kershaw. A Yaƙin Manassas na Farko, ƙwallon Minie ta buge shi kuma ya ji rauni sosai. Da yake farfadowa, an ci gaba da shi a matsayin colonel lokacin da Kershaw ya ci gaba da zama brigadier janar. Ayyukan farko na Kennedy a cikin umurnin rundunar ya faru ne a wani rikici a Nine-Mile Road kusa da Richmond, Virginia, a watan Yunin 1862 a lokacin yakin Peninsula. Bayan yaƙi a
Yaƙin Savage's Station, an kashe shi na makonni da yawa ta zazzabi. Ya koma ga rundunarsa a lokacin yakin Maryland. A lokacin Stonewall Jackson na zuba jari na Harpers Ferry, Kennedy ya kasance tare da brigade na Kershaw a cikin kama manyan Maryland Heights. Ya jagoranci rundunarsa a cikin Kershaw's counterattack a lokacin yakin Antietam, yana tuki wani ɓangare na Union II Corps a gabansa. Duk da haka, ya fadi da rauni sosai a cikin cajin farko, ya buga a cikin ƙafa da kuma Achilles tendon yayin da yake tsallake shinge na katako tare da Hagerstown Pike. Har ila yau, sake dawowa a lokaci don babban yakin, Kennedy ya jagoranci 2nd da 8th South Carolina don tallafawa Janar Howell Cobb a Marye's Heights, wanda ya fi mayar da hankali ga yakin basasa a Fredericksburg.