Rogers appeared on the 1954 Shelly Manne album The Three and the Two along with Jimmy Giuffre. Much of the music he recorded with Giuffre showed his experimental side, resulting in an early form of avant-garde jazz. He also made notable recordings with Art Pepper and Andre Previn, among others.
From 1953 through 1962 Rogers recorded a series of RCA Victor albums (later reissued under the Bluebird label) and Atlantic albums with his own group, Shorty Rogers and His Giants, including Shorty Courts the Count (1954), The Swinging Mr. Rogers (1955), and Martians Come Back (1955), the album title alluding to the tune "Martians Go Home" which Rogers had composed and performed on The Swinging Mr. Rogers earlier the same year. These albums incorporated some of his more avant-garde music. To some extent they could be classified as "cool" jazz; but they also looked back to the "hot" style of Count Basie, whom Rogers always credited as a major inspiration.
Credited with the composition of the music for UPA's Mr. Magoo cartoon Hotsy Footsy and the Looney Tune Three Little Bops, Rogers eventually became better known for his skills as a composer and arranger than as a trumpeter.
After the early 1960s Rogers stopped performing on trumpet, and left the jazz scene for many years. Among other composing and arranging activities, he arranged a series of records for The Monkees in the late 1960s, and in the 1970s contributed episode scores for the fourth season of Starsky & Hutch. Finally, in 1982, he was persuaded to pick up his trumpet and return to performing in jazz ensembles, playing first with Britain’s National Youth Jazz Orchestra and soon with Bud Shank and others. In the 1990s he formed a Lighthouse All Stars group along with Shank, Bill Perkins and Bob Cooper.