The park originally opened on 26 July 1975 by entrepreneur Eddy Meeùs. The park's name; "Walibi", is aabbreviated play-on-words of three local districts within the province of Walloon Brabant near where the park sits - Wavre, Limal, and Bierges. A Wallaby (a macropod cousin of the kangaroo) was used as the mascot of the park to fit in with its name. The park opened with children's attractions that were themed to the Belgian comic franchise Tintin, including The secret of the Unicorn   and Tintin in the jungle  , of which the park held the license until the end of 1995. The park also opened with a water skiing section which remained until 1994.

An indoor water park, Aqualibi, opened next door to the park in 1987.

In December 1997, with an interest to enter the European market and to compete with rival Disneyland Paris, the US-based Premier Parks (later Six Flags) announced that they would purchase a controlling stake in the Walibi Group from Eddy Meeùs. For 1998, the park opened up a new themed area based on the Lucky Luke franchise entitled "Lucky Luke City" which contained the world's largest drop tower attraction; entitled "Dalton Terror".. The addition of the area marked the last new addition to the park under Meeùs' control. For 1999, Premier added three new attractions to the park intending to make it the flagship of Six Flags' European operations.

Shortly after Premier rebranded under the Six Flags name, plans were put into place for the park potentially being rebranded under the Six Flags umbrella. On December 29, 2000, Six Flags officially announced that the park would be renamed as Six Flags Belgium. with the park's official renaming was put into place in January. The relaunch of the park would coincide with over $30 million worth of investments and changes with the most major being the addition of Warner Bros. properties into the park, including attractions based on Looney Tunes and DC Comics characters; while Walibi would be replaced with Bugs Bunny as the park's new mascot. Despite the Americanisation of the park, the Belgian-based Lucky Luke would remain. The rebranding of the park was put in place after sister park Walibi Flevo's rebranding as Six Flags Holland led to a heavy boost in attendance. The park officially reopened under its new name on 28 April, after a delay from its originally intended opening of 8 April. On 24 November 2001, Eddy Meeùs passed away at the age of 76.

Following financial difficulties and other issues, Six Flags announced the sale of their European Parks division to an undisclosed buyer on 15 March 2004. The purchaser was later revealed to be the London-based Palamon Capital Partners, who rebranded the chain as StarParks. The Warner Bros. license was not included in the sale. On April 16, Palamon announced that the park would rebrand back under the Walibi name for the 2005 season, following a fan-cast polling vote. At the end of the park's 2004 season on 7 November, it was announced that Six Flags Belgium would become Walibi Belgium upon the start of the park's 2005 season on 26 March, while Walibi would return as the park's mascot (although he had a semi-return at Aqualibi near the end of 2003(); having been on a four year "world tour" and being handed back the keys to the park from Bugs Bunny. A newly introduced group of characters (deemed his "world tour" friends) and a female counterpart named Walibelle were also introduced as part of the park's new storyline. These characters would appear in Walibi Folies, which would rebrand from Bugs Bunny Land, while the 3D cinema would replace the Looney Tunes show with SpongeBob SquarePants 4-D. Walibi's promotions director Dominique Fallon had proclaimed that former owner Eddy Meeùs had cited the Six Flags rebranding as a "mistake".

In March 2006, Palamon Capital Partners sold the Walibi chain, including Walibi Belgium, to Grévin & Cie, a subsidiary of Compagnie des Alpes. This was done for Palamon to focus its operations solely on sister park Movie Park Germany.

From 2012 to 2014, the Aqualibi waterpark underwent a major refurbishment, costing €11 million (US$16 million).

In March 2014, the park's license for Lucky Luke was not renewed.