When elected pope, Julius II promised under oath that he would soon convoke a general council. Time passed, however, and this promise was not fulfilled. Consequently, certain dissatisfied cardinals, urged, also, by Emperor Maximilian and Louis XII of France, convoked a council at Pisa and fixed September 1, 1511, for its opening This event was delayed until October 1. Four cardinals then met at Pisa provided with proxies from three absent cardinals. Several bishops and abbots were also there, as well as ambassadors from the King of France. Seven or eight sessions were held, in the last of which Pope Julius II was suspended, whereupon the prelates withdrew to Lyons.

The pope hastened to oppose this "conciliabulum" with a more numerously attended council, which he convoked, by a Papal bull of July 18, 1511, to assemble 19 April, 1512, in the Basilica di San Giovanni in Laterno. The Bull was at once a canonical and a polemical document. In it the pope refuted in detail the reasons alleged by the cardinals for their Pisa "conciliabulum". He declared that his conduct before his elevation to the pontificate was a pledge of his sincere desire for the celebration of the council; that since his elevation he had always sought opportunities for assembling it; that for this reason he had sought to reestablish peace among Christian princes; that the wars which had arisen against his will had no other object than the reestablishment of pontifical authority in the States of the Church. He then reproached the rebel cardinals with the irregularity of their conduct and the unseemliness of convoking the Universal Church independently of its head. He pointed out to them that the three months accorded by them for the assembly of all bishops at Pisa was too short, and that said city presented none of the advantages requisite for an assembly of such importance. Finally, he declared that no one should attach any significance to the act of the cardinals. The Bull was signed by twenty-one cardinals.

The French victory of Ravenna (11 April, 1512) hindered the opening of the council before May 3, on which day the fathers met in the Lateran Basilica. There were present fifteen cardinals, the Latin Patriarchs of Alexandria and Antioch, ten archbishops, fifty-six bishops, some abbots and gererals of religious orders, the ambassadors of King Ferdinand, and those of Venice and of Florence. Convoked by Julius II, the assembly survived him, was continued by Pope Leo X, and held its twelfth, and last, session on 16 March, 1517. In the third session Matthew Lang, who had represented Maximilian at the Council of Tours, read an act by which that emperor repudiated all that had been done at Tours and at Pisa. In the fourth session the advocate of the council demanded the revocation of the Pragmatic Sanction of Bourges. In the eighth (17 December, 1513), an act of King Louis XII was read, disavowing the Council of Pisa and adhering to the Lateran Council. In the next session (5 March, 1514) the pope published four decrees:

• the first of these sanctions the institution of ontes pietatis, or pawn shops, under strict ecclesiastical supervision, for the purpose of aiding the necessitous poor on the most favourable terms;
• the second relates to ecclesiastical liberty and the episcopal dignity, and condemns certain abusive exemptions;
• the third forbids, under pain of excommunication, the printing of books without the permission of the ordinary of the diocese;
• the fourth orders a peremptory citation against the French in regard to the Pragmatic Sanction. The latter was solemnly revoked and condemned, and the concordat with Francis I approved, in the eleventh session (19 December, 1516).
• Finally, the council promulgated a decree prescribing war against the Turks and ordered the levying of tithes of all the benefices in Christendom for three years.

Unfortunately, little was done to put the work of the council into practice. Some commentators have suggested that the Protestant Reformation could have been avoided if the reforms had been more energetically put into practice. In fact, Martin Luther's promulgation of the 95 theses occurred just seven months after the close of the Council.