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In 1987, a group of concerned parents and business people began to recognize the need for a nondenominational evangelical Christian school in the Cedar Rapids area. As a result of the vision of these people, meetings were held around the city to inform people about the needs and plans to begin a Christian school. These initial meetings in 1988 included Dr. Sam Warren, principal of Des Moines Christian School, and Roy Porter, past president of the Des Moines Christian School Board of Directors. These meetings also enjoyed the support of many local pastors, including Rev. Ed Bateman of Faith Bible Church, Rev. Richard Ernst of Hillside Wesleyan Church, Rev. Larry Jonson of Open Door Ministry, Rev. Alec Rowlands of First Assembly of God Church, Rev. Don Scarlett of First Church of the Nazarene, and Rev. Theoren Smith of Calvary Baptist Church. At the first meeting on January 16, 1988, more than 200 people were in attendance.
A steering committee elected officers on February 4, 1988. As the steering committee began its preparations for the new school, there was a strong commitment to work with all Bible-believing Christians. A plan was made to develop a statement of faith which included the foundational and basic doctrines of Biblical Christianity. Any individual who agreed with and held to the school's doctrinal position would be eligible to participate in any aspect of the program. There was also a strong commitment to holding the new school to a high academic standard. The steering committee appointed the first Board of Directors on December 20, 1988.

The newly formed Linn Christian Education Association (LCEA) purchased the Adams Elementary School (the current building) from the Cedar Rapids Community School Board on June 9, 1989. The school building was built in 1961 and contained 27,200 sq. ft. of space, but was no longer being used by the public school district. The Nehemiah Project was begun to help prepare the building for use as the future Christian school. Isaac Newton Christian Academy officially opened its doors on August 28, 1989, the first day of school. The enrollment for the K-6th school was 89 students. A K-8 program followed the next school year, and a preschool program was developed a few years after that. 
For many years, stakeholders have asked the Linn Christian Education Association Board of Directors to extend the school's programming to include a high school. The requests for a high school increased significantly. In order to give the matter due diligence, in 2015, the Board of Directors formed a High School Exploration Committee. This Committee was made up of nearly 40 members. The Committee found the need and support for a non-denominational Christian high school was strong in our community. After much deliberation and investigation, the Board of Directors voted unanimously in 2015 to add a high school. The 9th grade class was begun in the 2016-2017 school year. Subsequent grades were added, one grade at a time, over the following years until the entire high school unit (9th - 12th grades) was completed in the 2019-2020 school year. The first Senior class graduated in 2020.

The school was initially accredited by the Iowa Department of Education as a non-public school in 2004. The school was later accredited with the Association of Christian Schools International (ACSI) in 2013.  The school was unanimously approved by the ACSI Accreditation Commission for a full 5-year renewal of accreditation in 2019.  This accreditation establishes Isaac Newton Christian Academy as an educational institution which meets the high standards necessary for quality education in an authentic Christian setting.

The facility has grown over the years, as the school program has grown. After one building expansion project in 2000, the addition of The Patriot Center in 2015, and a large construction project on the core of the main building in 2017, the campus took its current size and shape.
In 2019, the school celebrated its 30th anniversary of its founding.  Throughout those 30 years, God has provided for the school, allowed it to grow and remain faithful in its mission to develop Christlike character and academic excellence in its students.
The school completed a total window replacement project in the original building, and a total remodel of the Pre-Kindergarten room during the summer of 2023.