François Annibal II d'Estrées (1623 - Rome, 30 January 1687) was a French nobleman and diplomat from the House of Estrées.
From 1671 until his death, he was French Ambassador to the Holy See under the pontificates of Clement X (1670–1676) and Innocent XI (1676–1689) and with residence in the Palazzo Farnese.
He received support from his younger brother César d'Estrées, who was appointed cardinal on 16 May 1672 and who also resided in Rome.
François Annibal II d'Estrées died of a stroke while serving as ambassador in Rome on 30 January 1687.
His body was brought to Soissons and buried there in the church of the Convent of the Feuillants, which his father had built as a family burial place.