1702, "to leave one's companions, go apart, retire, withdraw," from Latin secedere "go away, withdraw, separate; rebel, revolt," from se- "apart" (see se-) + cedere "to go" (from PIE root *ked- "to go, yield").
The sense of "withdraw from a political or religious alliance or union" is recorded from 1755, originally especially in reference to the ministers who left the Church of Scotland about 1733 (Seceders); later, in U.S. history, to the attempt by Southern states to separate from the union (1861). Related: Seceded; seceding.
From the Latin past-participle (secessus), English once had secess "a going away, withdrawal, retirement" (1560s), and Chauliac (early 15c.) has a noun secesse "purging of the bowels."