Geographically, Coconino County is part of the Colorado Plateau, a generally high wooded upland cut by many deep drainages. The elevation ranges from under 2,000 feet along the Colorado River at the western boundary of the county to 12,670 foot Humphrey's Peak in the San Francisco Mountains north of Flagstaff, the highest point in Arizona. Most of the county is between 4,000 and 8,000 feet elevation although precipitation ranges from less than 10 inches annually in the eastern portion of the county to over 25 inches in the Kaibab National Forest north of the Grand Canyon. The primary rivers in the northern and central portions of the county are the Colorado River and its tributaries, Kanab Creek and Little Colorado River, while the Verde River and its tributary, Oak Creek, drain the southern portion. Vegetation ranges from sparse grasslands to pinon-juniper scrub to ponderosa pine forest in most of the county to Douglas fir and spruce forests in the areas above 8,000 feet.

Geologically, the Plateau is very old and relatively stable. The Vishnu Schist in the bottom of the Grand Canyon has been radio metrically dated to two billion years old. Above that are layers upon layers of sedimentary rocks, interrupted occasionally by lava flows, igneous intrusions, and erosion unconformities. In Arizona the boundaries of the Plateau are clearly defined by the Grand Wash Cliffs in Mohave County on the west and the Mogollon Rim which forms part of the southern boundary of Coconino County. The current landforms are the result of millennia of weathering by wind and water. Resistant layers of sandstone often form the tops of cliffs and mesas, protecting the softer underlying layers of shale. Porous layers of limestone minimize surface runoff in some regions since the water sinks into underground aquifers instead. Volcanoes have produced many of the higher mountains, notably the San Francisco Mountains. Sunset Crater National Monument is the site of the most recent volcanic activity in Arizona. The cinder cones in the monument erupted around 1065 C. E. and spread a layer of fertile volcanic ash on the surrounding countryside which improved farming for the local peoples.

The earliest inhabitants of the area were nomadic hunters from the Great Plains who visited the area of the Little Colorado River between 10,000 and 13,000 years ago. Around 5000 B. C. E. the Anasazi Culture developed and started spreading across the Colorado Plateau region. Around 900 C. E. the Sinagua Culture developed in the vicinity of present-day Flagstaff. By about 1400 C. E. both groups were breaking up and disappeared from the region. By the arrival of the Spanish explorers in the 1600's, the tribes in the northern portion of present-day Arizona consisted of the Hopi, Havasupai, Pai (Yavapai and Walapai), and the Paiutes. Later the Navajo moved into the region from New Mexico.

The Spanish explored the region, but made no permanent settlements in modern-day Coconino County. Garcia Lopez de Cardenas was sent by Coronado to explore the "great river" west of the Hopi settlements and his expedition reached the Grand Canyon in 1540, but could not find a way into the canyon and returned to the Zuni pueblos where Coronado was. Several other explorers also started out from the settlements in Nuevo Mexico: Don Antonio de Espejo in 1583 crossed the Little Colorado and went as far west as the Verde River before turning back, Farfan in 1598 retraced much of Espejo's trail, Onate in 1604 crossed through on his way to the modern Bill Williams River which he followed to the Colorado and thence to the Gulf of California. In the 1770s Franciscan missionaries Silvestre Velez de Escalante and Francisco Atanasio Dominguez crossed the northern-eastern portion of Coconino County while missionary Fray Francisco Garces wandered through much the region south of the Grand Canyon.

During the 1850s, three U. S. military expeditions crossed through the region between the Little Colorado River and the upper reaches of the Verde River. Captain Lorenzo Sitgreaves of the Army Corps of Topographical Engineers mapped a possible wagon road to California through the area in 1851. Lieutenant Amiel W. Whipple surveyed a possible railroad route in 1853-1854. Ex-Navy Lieutenant Edward F. Beale was the leader of the next expedition in 1857. This was the famous "Camel Experiment" by which the military determined that camels were quite well suited to surviving in the "Great American Desert." Beale retraced much of Whipple's survey and the wagon road built along the survey route and used by some California-bound travelers bore Beale's name. Lieutenant Joseph C. Ives crossed the region from west to east on his way from the Colorado River to Fort Defiance (on the Arizona-New Mexico boundary). He made several side trips along the way, including one going down into the Grand Canyon with several Indian guides. After the Civil War was over, Major John W. Powell spent three years (1869-1871) exploring the Colorado River between Green River, Wyoming, and the western end of the Grand Canyon.

During the 1870s, Mormon settlers came into the region from the north. Their first settlement in Coconino County was at Lee's Ferry on the Colorado River which was a stopover on the trip to their towns on the upper Little Colorado River in what is now Navajo and Apache Counties. Fredonia, Jacob's Lake, Tuba City and Mormon Lake in Coconino County are among the towns first settled by Mormons.

With the 1880s the railroads and more settlers came to Coconino County. In 1883 the Atlantic & Pacific (later known as the Atchison, Topeka & Santa Fe) completed a line across Arizona to the Colorado River (and later to points west). Logging and cattle ranching developed as major industries in the area. In 1887 a branch line was started in Flagstaff to reach the mining areas around Globe, but it was never completed. In 1901 the Grand Canyon Railway was opened to provide service from Williams to the South Rim as tourism became a more profitable industry.

Starting in 1887 citizens in what was then northern Yavapai County attempted to have Frisco County created with the seat at Flagstaff. However, they remained part of Yavapai County until 1891 when Coconino County was formed with Flagstaff as the county seat. Although there was later an unsuccessful attempt to create Hunt County (with Williams as the county seat) from the western portion of Coconino, neither the boundaries nor the seat of Coconino have changed since it was formed.

Coconino County had a population of 75,008 people in the 1980 census, up substantially from the 48,326 people recorded in the 1970 census, but still placing the county in sixth place compared to the other counties. In 1900, for comparison, Coconino County had a mere 5,514 people and had increased to 23,910 by 1950. As of 2020  the county had a population of 145,101.