While the design team originally intended for the aircraft to be a straightforward stretched derivative of the Phenom 100, a clean sheet approach was later adopted.

The prototype Phenom 300 conducted its maiden flight on 29 April 2008, type certification was received on 3 December 2009, permitting its entry into service that same month.

During the early 2000s, Embraer was in the process of designing the Phenom 100 light business jet; while conducting market research, it was discovered that numerous potential customers were expressing a desire for a enlarged model of the aircraft.

Initial design work was focused on a straightforward scaling up of the Phenom 100, however, Embraer later concluded that a "clean sheet" approach was necessary, leading to the adoption of more powerful engines, spoiler-equipped swept wings, and detachable aluminium winglets.

[3] Various features from the Phenom 100 were transferred across, such as its relatively long structural life, an all-composite T-tail, trailing-link landing gear, fly-by-wire brakes, the Prodigy avionics suite, a cabin and cockpit interior designed by BMW DesignWorksUSA.

[3][5] On its second flight, made on 6 May, the prototype was flown from Gavião Peixoto to Embraer’s headquarters at São José dos Campos for further evaluation.

[6] On 29 December 2009, Embraer delivered the first Phenom 300 to Executive Flight Services at the company's headquarters at São José dos Campos, Brazil.

[7] On 31 January 2020, Embraer announced that it was implementing a package of upgrades to the Phenom 300; resulting changes included the maximum speed being increased from Mach 0.78 to 0.80 (446 to 464 kn, 826 to 859 km/h, 513 to 534 mph), expanded endurance from 1,992 to 2,010 nmi (3,689 to 3,723 km; 2,292 to 2,313 mi), and the rated engine thrust being raised from 3,360 to 3,478 lbf (14.95 to 15.47 kN) via the adoption of improved PW535E1 turbofan engines.

[3] To reduce complexity and potential for confusion, mix-mode anti-icing measures were avoided in favour of exclusively using a variable bleed air system to heat both horizontal wings while permitting a safe level of ice to accrete on the vertical stabiliser.

[3] To mitigate the aircraft's tendency to Dutch roll, a rudder on the ventral fin acts as a yaw damper.

[33] In March 2019, Embraer delivered the 500th Phenom 300, claiming more than half of the light jet market share since 2012; at the time it was being used in over 30 countries and had cumulative carried 2.5 million passengers across 600,000 flights and 800,000 hours.