He is the only child of his parents

The lone surviving son of Christopher Wren the Elder (1589–1658) and Mary Cox, the only child of Wiltshire squire Robert Cox of Fonthill Bishop, Wren was born in East Knoyle, Wiltshire. At the time, Christopher Sr. served as the rector of East Knoyle and, afterward, as the dean of Windsor. All three of their children were born when they were residing at East Knoyle; Mary, Catherine, and Susan were all born before the year 1628. However, several other infants who were born also perished within a few weeks of their birth. Their second daughter, Elizabeth, was born two years after the birth of their son, Christopher, in 1632. Although there doesn't seem to be a record left of the time, Mary must have passed away very soon after Elizabeth was born. The family did, however, experience financial success via Mary Cox since, as the sole heir, she received her father's wealth.

Wren "seemed consumptive" as a child. Despite being a sickly youngster, he would live to a ripe old age. His father and a private tutor tutored him at home in the beginning. Although his family spent a portion of each year at Windsor when his father was appointed by the monarch to the position of Dean in March 1635, nothing is known about Wren's time there. The Rev. William Shepherd, a local priest, taught him there for his first eight years of schooling.