The exact date of composition of this work is still largely unknown. The autograph manuscript has also been lost. However, a wide variety of sources have survived, due to Bach himself using it as essential teaching material, many of his pupils making copies, and his son Friedemann continuing to enjoy performing it in later years. These sources show subtle differences not only in the title and the presence or absence of the fugue, but especially in the arpeggios in the first half of the Fantasia. By the first half of the 19th century, it was already frequently taken up in publications, and in 1819, a version including dynamics, articulation, and ornamentation found in Friedemann's copy was published. (Later, Bischoff included this version as an alternative reading after critical examination of the sources. Whether Friedemann himself applied these ornamentations is doubtful given their stylistic characteristics.) In addition to the extremely numerous variant readings,Hans von Bülow published revised editions with alterations in the mid-19th century, complicating the source situation. Even the Bach Gesamtausgabe (Complete Works) was published with dynamics and slurs of unknown origin. Subsequently, the "Urtext edition" published by G. Henle Verlag, edited by Dadelsen, was long considered the most reliable score, but the New Bach Edition finally included this work in 1999 (V/9.2).

The existence of variant readings in copies and various practical editions indicates that the work was always transmitted through performance. Given the improvisatory passages in the Fantasia, it seems unsurprising that numerous variants emerged. However, stepping beyond the superficial elements such as seemingly arbitrary chromatic runs and dizzying variations of small motifs, and shifting attention to the harmonic progression and tonal development, one is astonished by the meticulousness of Bach's calculations in the musical structure. Utilizing dissonances, deceptive cadences, altered cadences, and enharmonic modulations, a diverse range of keys—sharp keys, flat keys, and at times even glimpses of major keys—are juxtaposed and connected with remarkable naturalness. Bach gave this to his pupils as teaching material because it possessed a high degree of perfection, serving as a model for composition.

Beethoven thoroughly studied this piece. This master, who perfected the Classical style and pioneered the Romantic, likely saw in the Chromatic Fantasia a sophisticated fusion of strict form and subjective expression. The fact that the Fantasia is followed by a Fugue also functions as a juxtaposition and sublation of two contrasting elements. Although the Fugue begins seemingly calmly, it accelerates in solemnity, finally presenting the theme majestically across a wide range, and concluding with a chromatic ascent across the keyboard. The anguish and despair expressed in the improvisatory Fantasia seem to be further heightened and concentrated as they are carried over into the strict compositional style of the Fugue.