The circumstances of Super Aguri's creation were rooted in Honda's restructuring of British American Racing at the end of the 2005 season. Honda completed its buyout of BAR and retained Jenson Button as lead driver, but replaced Takuma Sato — a popular figure in Japan — with Rubens Barrichello. Sato had scored only a single point across his second full season with the team. Public pressure in Japan and Sato's continued popularity persuaded Honda to assist him in continuing to race in Formula One, and this influence was central to the formation of Super Aguri and the securing of Honda engine supply.
Talks about starting the team began in February 2005. The team registered its intention to enter the 2006 World Championship with the FIA ahead of the governing body's November deadline, but the official entry list confirmed the FIA had not approved the entry, reportedly due to a failure to produce the required $48 million bond on time. Super Aguri re-applied in 2006 and needed unanimous agreement from the ten existing teams. The Midland team initially blocked the entry on the grounds of potentially reduced television revenue, but eventually the necessary agreement was secured and the FIA confirmed Super Aguri's entry on 26 January 2006.
The team entered 2006 using the SA05, an updated version of the 2002 Arrows A23 chassis, purchased from former Minardi principal Paul Stoddart who had acquired the cars when Arrows went into receivership. The technical side was overseen by former Arrows engineer Mark Preston, who brought many ex-Arrows mechanics with him. The cars were powered by customer Honda RA806E 2.4-litre V8 engines.
Takuma Sato was the primary driver, joined by Yuji Ide as his initial teammate. Ide's selection attracted attention due to his age — at 31 he was the oldest F1 rookie — his limited European racing experience, and his inability to speak English. At the San Marino Grand Prix, Ide was involved in a collision with Christijan Albers of Midland that sent Albers into a series of rolls. The FIA subsequently revoked Ide's Super Licence on 10 May 2006. Franck Montagny and then Sakon Yamamoto stood in before Sato secured a tenth-place finish at the Brazilian Grand Prix to close the season.
Super Aguri retained Sato for 2007 and signed Anthony Davidson, previously Honda's test driver, as his teammate. The car for 2007, the SA07, failed its initial FIA crash test and its launch was delayed to less than 48 hours before the first practice session in Australia. Despite the chaotic preparation, Sato and Davidson qualified tenth and eleventh for the Australian Grand Prix — the team's best qualifying performance to that point.
Controversy arose when rival teams Williams and Spyker challenged Super Aguri's use of a chassis closely based on the 2006 works Honda, citing Concorde Agreement regulations prohibiting the use of parts designed by another F1 manufacturer. The FIA declined to act without the matter being resolved in court.
The team's season highlight came at the Canadian Grand Prix, where Sato finished sixth and scored three points, passing defending world champion Fernando Alonso on track. At the Spanish Grand Prix Sato had scored the team's first-ever championship point with an eighth-place finish. All four of Super Aguri's World Championship points were scored by Sato in 2007.
Title sponsor SS United Group Oil and Gas Company defaulted on sponsorship payments during the season, forcing the team to shed around 30 staff and creating the financial fragility that would ultimately end the project.
Super Aguri entered 2008 with Sato and Davidson retained following the acquisition of an unspecified stake by the Magma Group. The SA08's launch was postponed in February due to uncertainty over the team's future. Magma subsequently pulled out of its proposed takeover.
The team competed in the opening four races of the season, including the Spanish Grand Prix, allegedly with financial assistance from Bernie Ecclestone. At Istanbul for the Turkish Grand Prix, Super Aguri's trucks and motorhomes were denied entry to the circuit. On 6 May 2008, Aguri Suzuki announced the team's immediate withdrawal from the 2008 FIA Formula One World Championship, citing the breach of contract by SS United Group as the trigger for the financial difficulties that made continued racing impossible. The team went into administration on 7 May 2008.
The team's assets were subsequently purchased by German businessman Franz Hilmer of Formtech GmbH. Hilmer applied unsuccessfully to enter the 2010 Formula One World Championship under the Brabham name.