Cushing Eells was born at Blandford, Massachusetts, on February 16, 1810. He was the son of Joseph and Elizabeth (Warner) Eells. Cushing Eells graduated from Williams College in 1834. He later entered East Windsor Theological Institute in Connecticut and graduated in 1837. Rev. Cushing Eells was licensed to preach December 14, 1836, and was ordained a year late as a Congregational Missionary to the Zulus in Africa, but the planned voyage there was affected by a war between the Zulu tribes, so the American Board of Commissioners for Foreign Missions instead sent him to the Oregon Territory.

Eells married Myra Fairbanks (daughter of Deacon Joshua and Mrs. Sally H. Fairbanks) on March 5, 1838, in Massachusetts. The Eells headed west the very next day to be missionaries to the Indians of old Oregon. Accompanying them were Elkanah and Mary (Richardson) Walker, William H. and Mary A. (Dix) Gray, and Rev. Asa B. and Sarah Gilbert (White) Smith. Two years prior, Marcus and Narcissa (Prentiss) Whitman and Henry and Eliza (Hart) Spalding, along with several others, had made the same journey. The Eells, Walkers, and Smiths arrived at the Cayuse winter lodge site of Waiilatpu along the Walla Walla River, which became the Whitman Mission, on August 29, 1838. Soon after, each family established their own mission, with Cushing and Myra Eells settling among the Spokane Indians at Tshimakain with the Walkers. A fire destroyed this first mission at Tshimakain, yet the Eells stayed in the area.

The deaths of the Whitmans and others at Waiilaptu in 1847 and the ensuing Northwest Indian Wars signified the end of the missionary efforts of the ABCFM by 1850. The Eells and Walkers were moved from Tshimakain under military escort to Oregon, and the Eells settled in Forest Grove for the next 14 years. In that time Cushing Eells taught at various schools in the Tualatin Plains, including the Oregon Institute, now Willamette University. He also instituted the Tualatin Academy, now Pacific University, in 1849. In 1859, the "upper country" that had been closed during the Indian Wars was re-opened, and Cushing soon headed to the Walla Walla Valley.

There Eells decided to build a school in memory of Marcus and Narcissa Whitman. The first classes were held in December 1859, at Waiilatpu. The actual seminary was constructed later in the nearby town of Walla Walla. During the summer of 1866, the first building of the Whitman Seminary was erected on a site purchased by Dr. Dorsey Syng Baker. The seminary opened the same year on September 14. For the first two years, Eells was the principal, though Rev. P.B. Chamberlain was first intended for the position. Eells simultaneously served as superintendent of schools for Walla Walla County. For several years, he traveled the Washington Territory, founding Congregational churches and schools and raising money for the seminary. The Washington Territorial Legislature, which had granted a charter to Whitman Seminary on December 20, 1859, issued a new charter on November 28, 1883, and changed it to Whitman College. Until an endowment allowed the college to be financially secure and survive, Eells made efforts to keep it alive, giving it 10,000 dollars during his life. He also willed a great portion of his property to Whitman College. Despite the financial and enrollment problems in the beginning, Eells' Whitman memorial – a small, provincial seminary – transformed itself over the years into a reputable secular college.

Until his last days, Eells continued to do missionary work and was actively involved with Whitman College. He died in Tacoma, February 16, 1893, at age 83, after having served 55 of his years as a missionary.