It is named for Frank R. Gooding, the 7th governor and a United States Senator from Idaho.

[3] After the Bonneville flood, Natives settled the area starting at least 12,000 years ago.

The Oregon Trail traversed Gooding County with many emigrants stopping at Salmon Falls on the Snake River to barter fish with the native population.

While Gooding County presently contains significant farming operations, it was the discovery of gold in 1862 that brought non-native settlement to the area.

Mining settlement in the area was quite small in comparison to the rush to the Boise Valley occurring at the same time.

The 1863 Census of Idaho Territory indicates there were 600 miners working Snake River mining operations, possibly covering the span of the river from the Hagerman Valley to Idaho Falls.

The U.S. Census of 1870 enumerated 28 residents for "Overland Road and Snake River"[6][7][8][9] At the time of Snake River mining operations, the mining settlements were under the jurisdiction of Idaho County, Washington Territory.

The Toponis and Hagerman Valley settlements became part of Logan County at its creation in 1889.

Logan county established the Bliss, Malad, and Toponis precincts containing 340 residents at the 1890 census.

The arrival of the 20th Century brought a significant increase in settlement at Wendell and Toponis.

[11] The boom in settlement is clearly reflected when comparing 1900 and 1910 U.S. Census data.

From 1900 to 1910, the Gooding precinct posted a 931% increase over the population listed for Toponis in 1900.

As of the 2010 United States Census, there were 15,464 people, 5,531 households, and 3,927 families living in the county.

It is in the catchment area, but not the taxation zone, for College of Southern Idaho.