Rubuta ci gaba ga wannan sakin layi - Branch ya shiga rundunar sojojin tarayya, a watan Mayu 1861, a matsayin mai zaman kansa a Raleigh Rifles. Daga baya a wannan watan ya karbi ofishin babban jami'in jihar, amma ya yi murabus don yin aiki a filin. A watan Satumba an zabe shi a matsayin colonel na 33rd North Carolina. An nada shi brigadier janar a cikin Janairu 1862. Bayan yakin New Bern, an haɗa brigade dinsa zuwa A.P. Hill's Division na Stonewall Jackson's Corps. Shi ne babban brigadier janar a sashen Hill. Brigade na Branch ya yi yaƙi a yakin Hanover Courthouse, Yakin kwana bakwai, Cedar Mountain, Manassas na biyu, Chantilly
, da kuma Harper Ferry