Webjet was founded by Rogério Ottoni in 2004, Webjet planned to start flying the MD-82 from Lion Air that was formerly registered PK-LMN. But due to Lion Air Flight 538 disaster, they changed to the 737-300. Webjet officially started operations on July 12, 2005 with a Boeing 737-300 operating services from Rio de Janeiro-Galeão to Porto Alegre, Curitiba and Salvador.

On January 17, 2006, it was sold to Jacob Barata Filho and Wagner Abrahão, owners of companies related to tourism and transportation in the State of Rio de Janeiro. The second aircraft was received in November of that year.

On June 25, 2007, Webjet was again sold to CVC Viagens, the biggest Brazilian tour operator. CVC wanted to reduce its dependence on regular carriers, particularly on TAM Airlines. In December 2007 the third aircraft was received and since then new aircraft have been regularly added to the fleet, increasing destinations and frequencies.

On February 13, 2009, Wagner Ferreira took Paulo Enrique Coco's CEO position. He immediately implemented a few changes to make Webjet more competitive: on March 9, scheduled flights to Ilhéus, Maceió and Porto Seguro ceased and became regular charter destinations; on April 27, flights from Rio de Janeiro-Santos Dumont to Brasília, São Paulo-Guarulhos, and Belo Horizonte-Confins were added, but Webjet still kept operating from Rio de Janeiro-Galeão; a new logo and slogan were unveiled on that same day.

On February 11, 2010, Wagner Ferreira left the presidency of Webjet and Julio Rudge Perotti, the Vice-President Operations took over his position. In July 2010, Fernando Sporleder joined the airline as Vice-President Operations from the same position at TAM.

On September 27, 2010, after the airline cancelled more than 50% of its flights scheduled for the day, the National Civil Aviation Agency of Brazil (ANAC) ordered the suspension of ticket sales for 5 days to investigate reasons. After this period, sales and operations resumed as scheduled.

Although in Brazil Webjet informally used the prefix WJ for its flight numbers, officially it had been assigned by IATA the code WH.

On April 2011 it was reported that the owners of CVC, Carlyle Private Equity Fund (63,6%) and Guilherme Paulus (36,4%), were in conversations with TUI AG to possibly sell part of their participation in CVC to the German tour-operator. Since CVC was the owner of Webjet, should the transaction go ahead, Webjet would have been directly impacted.

Instead, on July 8, 2011, VRG Linhas Aéreas, owner of the brands Gol and Varig, announced the intention to purchase full control of WebJet Linhas Aéreas. The purchase contract was signed on August 2, 2011. On October 10, 2012 the purchase received its final approval with some operational restrictions from the Brazilian regulatory agency. Both companies continued to operate independently, however it was announced that in 2013 the Webjet brand would cease to the exist and will be completely integrated into Gol. Integration started in October 2012 when sales requested via Webjet's website started to be redirected to Gol's site.

On November 21, 2011, GOL Linhas Aereas announced that in December 2011, the renovation of Webjet's fleet would also start and would be completed within 12-18 months. All Boeing 737-300s would be replaced by Boeing 737-800s.

However, on November 23, 2012 Webjet abruptly ceased operations and all its services were incorporated by Gol, with the loss of 850 jobs, including pilots, cabin crew, airport and administrative staff. Passengers with Webjet tickets would be rebooked to Gol flights at no extra cost. Webjet's entire fleet was grounded and Gol announced its intention to return all 737-300s to lessors until the end of the first quarter of 2013, while the 737-800s are returned to Gol at the same time.

As of September 2012 Webjet Linhas Aéreas operated scheduled services to the following destinations:

As of November 2012, the fleet of Webjet Linhas Aéreas included the following aircraft: