Rubuta ci gaba ga wannan sakin layi - Bayan jihar Mississippi ta rabu da shi kafin fara yakin basasa, Barksdale ya yi murabus daga Majalisa don zama babban jami'in, sannan kuma babban jami'in, na Mississippi Militia, a matsayin brigadier general, tare da kwanan wata na Maris 1, 1861. A ranar 1 ga Mayu, an nada shi a matsayin colonel a cikin Sojojin Tarayyar Amurka na 13th Mississippi Infantry, wani rukunin da ya jagoranci a yakin farko na Bull Run a wannan bazarar, da kuma yakin Ball's Bluff a watan Oktoba. A cikin bazara mai zuwa, ya ɗauki rundunarsa zuwa Virginia Peninsula kuma ya yi yaƙi a cikin Kamfen na Peninsula da Yakin Kwanaki Bakwai. Lokacin da kwamandan brigade, Brig. Janar Richard Griffith, ya ji rauni sosai a yakin Savage Station
a ranar 29 ga Yuni, 1862, Barksdale ya karbi umurnin brigade kuma ya jagoranci shi a cikin jaruntaka, amma jini da banza, a yakin Malvern Hill. An san brigade a matsayin "Barksdale's Mississippi Brigade". An daukaka shi zuwa brigadier janar a ranar 12 ga Agusta, 1862.