After the Nationalist government came to Taiwan in 1949, he responded to the call to defend Taiwan and joined the military. But he found the regimented life of the army difficult to accept, and went on the run. He hid for 18 months before turning himself in to accept his punishment. By the time he got out, he was 26.
國民政府遷台之後，年輕熱情的柯錫杰響應「保衛大台灣」的號召，參加四千五百人的集體入伍，卻因無法適應軍中刻板的生活與教條似的訓練，竟然開了小差，從模範兵成了逃兵，在外面整整躲了十八個月，才回軍中自首接受處分，退役時已經二十六歲了。