Carroll Shelby's motivation to build the coupe grew from a specific aerodynamic deficit. After winning Le Mans in 1959, Shelby wanted to return and beat Ferrari with a car of his own construction. The AC Cobra was fast in the corners, but on the 3.7-mile Mulsanne Straight at Le Mans the open roadster was limited to around 157 mph — nearly 30 mph slower than the Ferrari 250 GTO, which held approximately 186 mph. That speed differential translated into a loss of over 10 seconds per lap, negating the Cobra's power advantage through the slower sections.
Shelby assigned Pete Brock to design the aerodynamic bodywork and Bob Negstad to handle the suspension and chassis. Working at the Shelby American shop in Venice, California, Brock developed the design by placing driver Ken Miles in a stripped chassis and building the windscreen and body formers around him in wood and tape, then hand-fabricating the aluminium bodywork. Before the car reached the track, Shelby consulted aerodynamics specialist Ben Howard of Convair, who recommended extending the tail by at least three feet. Brock stood by his original design. Miles took the first prototype to Riverside Raceway and recorded 186 mph on the main straight; after 30 further days of development the car was clocked at over 190 mph.
The first prototype was designated chassis CSX2287 and was built entirely in California. The remaining five coupes were completed at Carrozzeria Gransport in Modena, Italy.
The Shelby Daytona Coupes debuted at the Daytona Continental 2000 km in February 1964, where Dave MacDonald took pole position. The cars competed across a demanding calendar of 500 km, 1000 km, 2000 km, and 24-hour events on the International Championship for GT Manufacturers, including races at Le Mans, Daytona, Sebring, Imola, Reims, Spa-Francorchamps, Goodwood, Oulton Park, the Tour de France Automobile, Enna, Rouen, Monza, and the Nurburgring.
In 1964 the coupes claimed notable class victories: Dave MacDonald and Bob Holbert won the GT class at the 12 Hours of Sebring, and Dan Gurney and Bob Bondurant took GT class honours at the 24 Hours of Le Mans, finishing fourth overall. Despite these results, the Shelby team finished second in the GT III championship, six points behind Ferrari.
In 1965 the Shelby Daytona Coupes returned and dominated the GT III class across the season. Class wins came at the 24 Hours of Daytona, the 12 Hours of Sebring, the Italian Grand Prix at Monza, the Nurburgring 1000 km, and the Enna-Pergusa race. The championship was clinched at the 12 Hours of Reims on 3–4 July 1965, where Bob Bondurant and Jo Schlesser drove chassis CSX2601 to GT III class victory. The final margin over the opposition was 19 points.
Carroll Shelby was also reassigned to the Ford GT40 project during 1965, which explains why the Daytona Coupe programme concluded after just two seasons.
The first prototype accumulated an extensive race record at Daytona, Sebring, Reims, Spa-Francorchamps, Oulton Park, Le Mans, Tour de France, and Bonneville. Drivers included Dave MacDonald, Bob Holbert, Phil Hill, Chris Amon, Jochen Neerpasch, and Innes Ireland, among others. At Le Mans in 1964 the car led the GT class before being disqualified in the tenth hour for an illegal jump start caused by battery and alternator failure. In November 1965, Brock's prototype set 25 USAC/FIA world speed records at the Bonneville Salt Flats, driven by Craig Breedlove, Bobby Tatroe, and Tom Greatorex during a Goodyear tyre testing session.
After its racing career, CSX2287 passed through several owners including music producer Phil Spector, who drove it on public roads before legal problems led him to sell it. The car disappeared from records by the mid-1970s and was feared destroyed. In 2001 it was rediscovered in a storage unit in California following the death of its last known owner. After extensive legal proceedings, the car was acquired by Dr. Frederick A. Simeone and is now part of the permanent collection at the Simeone Foundation Automotive Museum in Philadelphia. In January 2014 CSX2287 became the first vehicle added to the Historic Vehicle Association's National Historic Vehicle Register, and simultaneously the first automobile recorded under the United States Secretary of the Interior Standards for Heritage Documentation, with its record held at the Library of Congress. In November 2014 it won the International Historic Motoring Awards Car of the Year, the first American car to receive the honour.
The second coupe completed entered nine FIA races across the two seasons, winning four: Le Mans 1964 (GT class, with Gurney and Bondurant clocking over 196 mph on the Mulsanne Straight), the RAC Tourist Trophy 1964, Daytona 1965, and Sebring 1965. It is currently displayed at the Shelby American Collection in Boulder, Colorado.
Leased to Ford of France and entered as the French national entry at the 1965 Nurburgring 1000 km, finished third in GT III class driven by Andre Simon and Jo Schlesser. Carroll Shelby personally owned this car before it was sold at auction by RM Auctions for $4.4 million in August 2000.
Won four FIA GT III class events in 1965 — Monza, Nurburgring, Reims, and Enna — and clinched the 1965 championship at Reims. After being driven by Bob Bondurant in the film Red Line 7000, the car sold at auction for $7.25 million in August 2009.
The Shelby Daytona Coupe achieved what Carroll Shelby had set out to do: beat Ferrari in the GT class at international level. Shelby became the first American constructor to win a title in the FIA World Championships. In 2015 Shelby American announced a limited run of 50 continuation Daytonas to mark the 50th anniversary of the 1965 championship win. The car's aerodynamic philosophy also influenced later Shelby-Ford collaborations including the Ford Shelby GR-1 concept of 2004. The original prototype CSX2287 remains the most documented surviving example, its place in American automotive history confirmed by federal heritage designation.