Kammala wannan jumla: Rowley ya yi aiki a matsayin colonel na 13th Pennsylvania Infantry daga Afrilu 25, 1861, zuwa Agusta 6 na wannan shekarar. Daga nan sai ya zama colonel na 102 na Pennsylvania Volunteer Infantry Regiment. An ji masa rauni a
Yaƙin Bakwai Bakwai, yayin da yake jagorantar rundunarsa a cikin Sojojin Potomac. Ya jagoranci brigade a cikin VI Corps a yakin Fredericksburg. An gabatar da shi zuwa matsayi na brigadier janar zuwa matsayi daga Nuwamba 29, 1862, Rowley na gaba ya umurci brigade na I Corps a yakin Chancellorsville. Ya kasance mai kula da kwamandan na 3rd, I Corps a farkon yakin Gettysburg, yayin da Maj. Janar Abner Doubleday ya zama kwamandan kwamandan. (Chapman Biddle ya jagoranci tawagar Rowley.) A ranar 1 ga Yuli, 1863, rundunar ta yi fama da mummunan rauni da ke fuskantar 'yan Confederates daga Maj. Janar Harry Heth. An jefa shi daga dokinsa a lokacin da ya janye lokacin da ya tsaya a gajeren lokaci a kogin. Marar lafiya da kamuwa da cuta daga tafasa girman kaza qwai a ciki cinya, ya kasance mai zazzabi, kuma temperamental. Bayan wani rikici tsakanin Rowley da Brig. Janar Lysander Cutler a kan halayyar wasu daga cikin jami'an Wisconsin na 7, Cutler ya gabatar da zargin shan giya a watan Afrilu 1864. An ba shi kasa da awanni 24 don shirya kariya don shari'a, an yanke wa Rowley hukunci ta kotun soji wanda marubucin John F. Krumwiede ya ce, "rashin nuna bambanci da yin tafiya zuwa ga kansa". Kodayake an sake dawowa da sakataren War Edwin M. Stanton da Shugaba Abraham Lincoln, an ba Rowley kawai umarnin gundumar a yammacin Pennsylvania, saboda rikici tsakanin kwamandan sojojin Janar George G. Meade da kuma kwamandan kwamandan Janar Gouverneur K. Warren. An hana shi ta hanyar ayyukan Janar Darius N. Couch a kokarin dakatar da mamayewar 1864 na Pennsylvania da Janar Janar Jubal Early ya yi, ya yi murabus daga mukaminsa a ranar 29 ga Disamba, 1864.