Emeric was born in Késmárk in Royal Hungary (now Kežmarok in Slovakia) on 25 September 1657 as the fifth son of Count István Thököly and Mária Gyulaffy. His father was one of the wealthiest aristocrats in Upper Hungary (in present-day Slovakia); his mother was the granddaughter of Stephen Bethlen, who had been prince of Transylvania in 1630, she was related to three princes of Transylvania. Being his parents' only son to survive childhood, Emeric inherited when he was still a child his mother's estates in the Principality of Transylvania in 1659. His uncle, Count Francis Rhédey, Prince of Transylvania who died in 1667, also bequeathed his domains in Máramaros County to Emeric. A significant part of Emeric's inherited lands were located in Máramaros County. István Thököly persuaded Michael I Apafi, Prince of Transylvania, to make Emeric the "ispán" (or head) of the county in 1667. Actually, Apafi's influential counselor, Mihály Teleki, administered Máramaros on behalf of the minor "ispán".