There are few details known about John Johnson's early years. He must have developed a talent on the lute in his early childhood: a 16th century document dealing with composer/lutenist Daniel Bachelar (born, c. 1574) indicates that at the age of seven Johnson became an apprentice to a professional lutenist. The two probably served in the house of a nobleman or wealthy patron.
In 1579 Johnson secured the highly-coveted post of one of three lutenists to Queen Elizabeth. The other two were Mathias Mason and Thomas Cardell, respected musicians both. Though the number of royal lutenists would often swell to a half-dozen or more, Johnson would come to be the Queen's favorite among them.
He apparently wrote music throughout most of his adult years, typically scoring his works for solo lute or lute duet in the form of pavanes or galliards, or as arrangements of popular tunes or folk tunes. A pair of ballads appearing in 1588 used the music from two of Johnson's works, Flat Pavane and The Medley. This would suggest that Johnson's two pieces had already become popular with the public, their music, then, likely dating back to the 1570s or even 1560s. Numerous other compositions by Johnson were arranged by his contemporaries and by younger composers: Giles Farnaby (c. 1565-1640), for example, made a brilliant keyboard arrangement of Flat Pavane.
Johnson remained in the service of Queen Elizabeth until his death in 1594. He was well-liked and apparently quite content in his post as a royal lutenist: indeed, there is no evidence he ever left his homeland.