Koukoudeas was born in Üstrümce, then part of the Ottoman Empire (now Strumica, North Macedonia) at the end of the 19th century. He came from an old and important family of Strumica. Famous relatives of him were the violinist Dimitrios Koukoudeas or Semsis and the teacher of Strumica's Girls' School, Aikaterini Koukoudea. After graduating from the Greek school in his hometown, he travelled to Athens in 1905 to escape the Bulgarian attacks and to be enrolled in the armed groups being gathered for the Macedonian Struggle. He was also enlisted in the Hellenic Navy as a leading seaman.