Sarafis was born at Trikala in 1890 and studied law in the University of Athens. During the Balkan Wars, he enlisted in the Greek Army as a sergeant and was promoted to lieutenant in 1913. He became a Venizelist and played an active role in the various military conspiracies that were formed during the troubled 1920s. He participated in the two failed Venizelist coup attempts of 1933 and 1935. The latter was led by Nikolaos Plastiras and intended to overthrow the government of Prime MinisterPanagis Tsaldaris. The failure of the coup resulted in the execution of its leader for treason and dishonorable discharges for several of the participants. Sarafis himself was condemned to life imprisonment but was pardoned by the government.
Sarafis was exiled to the island of Milos which was populated but had no connection to military activities. He was thus effectively isolated from possible contacts with active Army members. In 1938, Sarafis was introduced to Marion Pascoe, an English student of the University of Oxford who visited the island to pursue her studies of archaeology. However, her limited knowledge of the Greek language prevented her from effectively communicating with the locals. Sarafis was reportedly the only person on the island with working knowledge of the English language and volunteered to help her in communicating. Their private conversations over political beliefs and the History of Greece resulted in her lifelong interest in Greek matters. Marion later claimed to have fallen in love with Sarafis at this point.
Marion left Greece during the Greco-Italian War. Sarafis resurfaced as a leading figure of the Greek Resistance movement. Initially in contact with the Republican EDES and EKKA movements, in March 1943 he was arrested by guerillas of the communist EAM/Greek People's Liberation Army. Despite his background, a month later Sarafis joined ELAS. His motives for this have been hotly contested, but he seems to have been impressed by ELAS' strength and at least partly sympathised with its political aims. In May, he was appointed as head of its general staff. From this position, he played a crucial role during the Resistance and later during the Dekemvriana. After the military and political defeat of EAM in the Dekemvriana, he was captured and exiled to Serifos where Marion re-established correspondence with him in 1946. She had joined the League for Democracy in Greece in England, which campaigned for the release of political prisoners and reform of British policy towards Greece.