Despite this, the Pratts remained at Nauvoo. When Orson later received a letter from one of Joseph Smith's detractors seeking to enlist his support, Pratt took the letter to Smith. This show of loyalty restored their friendship, and on 20 January 1843 church leaders declared Pratt's excommunication illegal, reinstated him in the church, and reappointed him as an apostle.

Concerned with protecting his people's rights, Smith sent Pratt to Washington, D.C., in March 1844. There Pratt published the Prophetic Almanac. When he learned in late July that Smith had been assassinated the previous month he returned to Illinois. In Nauvoo, the apostles defended their right to leadership of the church, worked to complete the temple, and introduced the Saints to the temple ceremonies. Meanwhile, Orson Pratt went to New York to preside over the church there and to publish The Messenger.

Returning to Nauvoo in December, Pratt found church leaders preparing to leave the city. He moved his family across the Mississippi River early the next year and then helped guide the pioneers to the Rocky Mountains. On 21 July 1847 he became the first Mormon to enter the Salt Lake Valley. The following year, Pratt returned to England, where he presided over the European Mission and edited The Latter-day Saints' Millennial Star.