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-) + concilare "make friendly" (see conciliate).
Reflexive sense of "become reconciled" is from late 14c. Meaning "to make (discordant facts or statements) consistent, rid of apparent discrepancies" is from late 14c. Related: Reconciled; reconciling.