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Born and raised in Vail, Colorado, Johnston was the son of Vail mayor Paul Johnston. He attended kindergarten through 12th grade at Vail Mountain School, graduating in 1993.  Johnston then attended Yale University, earning his bachelor's degree in philosophy in 1997. Throughout high school and college, Johnston was engaged in community service activities, including volunteering at a Denver homeless shelter and mentoring youth in a New Haven housing project. After graduating from college, Johnston taught at a rural high school in Greenville, Mississippi for two years as part of the Teach for America program; he wrote the book In the Deep Heart’s Core about his experiences. He then earned a master's degree in education policy from Harvard University. While at Harvard, Johnston worked with Al Gore education advisor John Schnur; with Schnur and others, he helped found New Leaders for New Schools, an organization dedicated to training and recruiting leaders for urban schools. After graduating from Harvard, Johnston went on to earn a law degree from Yale, and began advising political candidates on education policy, including Colorado U.S. Senate candidate Tom Strickland in 2002.

Returning to Colorado in 2003, Johnston was hired by the Joan Farley Academy, and then Johnston helped found MESA: Mapleton Expeditionary School of the Arts, a public school in Thornton, Colorado, in 2005. As the school's principal, he helped develop the school's curriculum and program as the school district shifted to developing smaller schools; he also oversaw improvements in the school's performance, including improving the senior class's college acceptance rates from 50% to 100% over three years. During his presidential candidacy, Sen. Obama visited the school in May 2008, where he delivered a major address on education; the school's and Johnston's achievements were also highlighted in a October 2008 campaign advertisement.

Following Hurricane Katrina, Johnston helped lead an education summit in New Orleans and worked with U.S. Rep. George Miller on legislation to recruit and retain teachers. Johnston joined the campaign of U.S. Senator Barack Obama as an informal advisor early in 2007, and, by May 2008, he was regarded as one of Obama's key advisors on education issues.

Johnston, his wife, Courtney, and their two children live in the Stapleton neighborhood of Denver.