The area was pioneered by Donald Fleming who, in partnership with Arthur Nicol, took up land in the area including Gnaraloo, but at the time it was known as Flemington. He later sold it to Frank Mottram but stayed in the area until 1935.
In 1908 the station was 90,000 acres (36,422 ha) in size and was held by Forrest, Emanuel and Co. who paid a £70 rental on the property.
Mottram was the owner in 1910 and the station was running about 1,500 sheep with the flock increasing in size to 3,554 in 1911 despite no stock being bought in that time. Following a good season another 800 lambs were tailed in 1912 increasing the size of the flock further.
The Mottram's sold the lease in 1921 with a flock of 9,000 sheep and now encompassing an area of 190,000 acres (76,890 ha) with the lease due to expire in 1948. The property was advertised with 70 miles (113 km) dividing it into 12 paddocks with 9 wells, 8 with windmills, tanks and troughs. The homestead had 3 large rooms, an office and a store room with a detached stone kitchen.
The station had a good year in 1922 with 9,000 sheep shorn and with an estimated 1,500 stragglers to be mustered and clipped. 223 bales of wool were produced, and the stock were all reported to be in good condition.
Messrs Powell and Cordes sold the station in 1927 to a partnership between Alex Fleming and Baden Powell. The station was sold in 1928 when the Gnaraloo Pastoral Company formed between the Fleming and Powell families was dissolved; the Fleming family came to own the station outright again with Donald's son, Alex Fleming owning the station from 1928 until at least 1954.
The area received heavy rains in 1953 with Gnaraloo being deluged with 610 points (6.1 in, 155 mm) of rain over two days. Surrounding station received falls of up to 3 inches (76 mm).
In 1988 Gnaraloo was purchased by Hakko Sunbay a Japanese Company with the idea of developing the tourism opportunity. Unfortunately the partnership failed and after 1 year of working the building was stopped leaving 32 unfinished cabins.
In 2005 Gnaraloo was sold to Paul Richardson who still owns and runs the Station. 21 of the cabins have been completed to date.
Gnaraloo station commenced its turtle conservation program in 2008 under the guidance and direction of the WA Department of Environment and Conservation (DEC).
January 2009 saw lightening start a fire at the southern boundary of Gnaraloo, the fire burned for 6 days and burnout 160 000 acres of the property. Stock numbers were reduced to 800 to protect the remaining vegetation.
On 18th December 2010 a monsoonal low crossed Gnaraloo Bay dropping 355mm of rain in one day.
In 2010 the station earned mention in the Clean Beach awards for 2010.