He was appointed an Auxiliary Bishop of Rome with the titular see of Vicohabentia on 3 July 1998 and was consecrated a bishop by Cardinal Camillo Ruini on 12 September 1998.

He was president of the diocesan commission on ecumenism and interfaith relations.
He worked in the Congregation for the Doctrine of the Faith and in the Congregation for the Causes of Saints.
He was said to have collaborated in the publication of Fides et Ratio in 1998.

He was named rector of the Lateran University on 18 January 2002.
On 8 September 2002, he was named a member of the Congregation for the Doctrine of the Faith.

During the Muhammad caricature controversy of 2005, Fisichella said that the freedom of the press was not absolute and not meant to be used against others.
He was a friend of Oriana Fallaci.
In 2005, he celebrated the 100th anniversary of the catechism of Saint Pius X.
When asked in 2005 if he would give Communion to Italian politicians Romano Prodi and Pier Ferdinando Casini, Fisichella responded that he "did not see a reason" for refusing Communion to Prodi, whereas Casini "knows well the rules of the Church" and does not present himself for Communion.
He was appointed an Auxiliary Bishop of Rome with the titular see of Vicohabentia on 3 July 1998 and was consecrated a bishop by Cardinal Camillo Ruini on 12 September 1998.
He was president of the diocesan commission on ecumenism and interfaith relations. He worked in the Congregation for the Doctrine of the Faith and in the Congregation for the Causes of Saints. He was said to have collaborated in the publication of Fides et Ratio in 1998.
He was named rector of the Lateran University on 18 January 2002. On 8 September 2002, he was named a member of the Congregation for the Doctrine of the Faith.
During the Muhammad caricature controversy of 2005, Fisichella said that the freedom of the press was not absolute and not meant to be used against others. He was a friend of Oriana Fallaci. In 2005, he celebrated the 100th anniversary of the catechism of Saint Pius X.
When asked in 2005 if he would give Communion to Italian politicians Romano Prodi and Pier Ferdinando Casini, Fisichella responded that he "did not see a reason" for refusing Communion to Prodi, whereas Casini "knows well the rules of the Church" and does not present himself for Communion.
Rino Fisichella