Most of what we know about Walther's life derives from his autobiography, published by Johann Mattheson in his Grundlage einer Ehren-Pforte (1740), and from Walther's extant letters.
Walther was born in Erfurt, Thuringia, in 1684. He had lessons with two organists in his native city, Johann Bernhard Bach (a distant relative of Johann Sebastian) and Johann Andreas Kretschmar. During his infancy, between 1678 and 1690, Erfurt had been home to the great South-German organist Johann Pachelbel. Walther's first contact with the Pachelbel tradition was through Pachelbel's Erfurt pupil Johann Heinrich Buttstett. The lessons with Buttstett were a disappointment (and Walther does not mention Buttstett in his autobiography); a text-book was more profitable. Three of these four masters are represented in the manuscript: J.B. Bach with four titles, Buttstett with seven, and Pachelbel with nineteen (not counting uncertain attributions).
In 1703 Walther embarked on his ‘Wanderjahre'. Important were the contacts he established with the distinguished music theorist Andreas Werckmeister in Halberstadt. With Werckmeister he kept a "pleasant correspondence", and the theorist provided him with works by the great representative of the North-German organ tradition, Dieterich Buxtehude (the manuscript contains 21 of his compositions). In 1706 Walther contacted Johann Pachelbel's son, Wilhelm Hieronymus, in Nuremberg.
This life of a wandering student ended in 1707, when Walther secured the post of organist at the Stadtkirche St Petri und Pauli in Weimar, not far from Erfurt. This turned out to be the end station of his career. Besides serving the church, Walther was active as a teacher to members of the ruling house of Saxe-Weimar and other high-class pupils. In 1721 Walther joined the court chapel as Hofmusicus; after that he made no further advancement.
Just one year after Walther's settlement in Weimar, his cousin Johann Sebastian Bach was appointed court organist and Cammermusicus in the same city. The relation between the two musicians, who were of nearly the same age, seems to have been close. Both copied each others' works. They shared at least one student, Johann Tobias Krebs (in this manuscript with one work). In 1712 Bach became godfather to Walther's second son (and third child). Of Walther's eight children, only four survived; his younger son Johann Christoph (1715-1771) followed in his father's footsteps as an organist.
The stand-still in Walther's career as a performing musician turned into a sad decline. The number of his pupils diminished, and he was passed over for vacancies such as the one created by Bach's departure in 1717 (Bach was dismissed after a month imprisonment). Since 1745 ill health made it impossible for Walther to fulfil his professional duties. Johann Christoph, called back from the university of Jena to substitute for his father, was not allowed to succeed him officially.
Of Walther's oeuvre we have incomplete knowledge. Apart from the organ works, only one vocal work survives complete. Most of his organ works are chorale settings . They range over a variety of forms, from simple three-part settings to more elaborate chorale partitas, fantasias and chorale fugues. According to Mattheson, Walther was Pachelbel's most worthy successor, "rightly to be called the second, if not artistically the first Pachelbel". According to the more recent appraisal by George J. Buelow:
Walther's chorale variations are uniformly of the highest merit, perhaps the only ones comparable to Bach's examples of the genre [...] Walther's sensitivity to the affective connotations of the melodies, his rich harmonic variety, the brilliant keyboard technique rooted in motivic counterpoint, and the strength of the contrapuntal ideas are all worthy of comparison with Bach's organ chorales.
 J.G. Walther: Briefe, hrsg. von K. Beckmann und H.-J. Schulze (Leipzig, 1987). Most of these are addressed to Heinrich Bokemeyer, cantor in Wolfenbüttel, and a faithful pen friend.
 O. Brodde: Johann Gottfried Walther: Leben und Werk (Kassel 1937), p. 5, 6
 J. Mattheson: Grundlage einer Ehren-Pforte (Hamburg 1740), p. 388
 J.G. Walther: Musicalisches Lexicon (Leipzig 1732), p. 345
 First edited by M. Seiffert in DDT, Vol. XXVI-XXVII (Leipzig 1906); new edition by K. Beckmann, Sämtliche Orgelwerke (Wiesbaden 1998-99).
 "[...] mit Recht der zweite, wo nicht an Kunst der erste Pachelbel". J. Mattheson: Der vollkommene Capellmeister (Hamburg 1739), p. 476
 G.J. Buelow, article Walther, Johann Gottfried, in Grove Music Online, Oxford Music Online, 20 Apr. 2010