mid-14c., reconcilen, transitive, in reference to persons, "to restore to union and friendship after estrangement or variance," also of God or Christ, "restore (mankind, sinners) to favor or grace," from Old French reconcilier (12c.) and directly from Latin reconcilare "to bring together again; regain; win over again, conciliate," from re- "again" (see re-) + conciliare "make friendly" (see conciliate).
Reflexive sense of "become reconciled, reconcile oneself" is from late 14c. Meaning "to make (discordant facts or statements) consistent, rid of apparent discrepancies" is from 1550s. Mental sense of "make (actions, facts, conditions, etc.) consistent with each other in one's mind" is from 1620s. Sense of "bring into acquiescence or quiet submission" (with to) is from c. 1600. Related: Reconciled; reconciling.