Mendelssohn claimed to have been inspired to write the symphony during his first visit to Britain in 1829. After a series of successful performances in London, Mendelssohn embarked on a walking tour of Scotland with companion Karl Klingemann. On 30 July, Mendelssohn visited the ruins of a chapel at Holyrood Palace in Edinburgh, where he had his initial idea for the piece. He described the experience in a letter, in which he included a draft of the symphony's opening theme. Mendelssohn and his companion later visited Staffa, which inspired the composer to write the Hebrides, a task which occupied him until its completion in 1830.
After completing the Hebrides, Mendelssohn continued to work on his initial sketches of what would become Symphony No. 3 while touring Italy. However, he struggled to make progress, and after 1831 set the piece aside.
Mendelssohn returned to the symphony in 1841 and completed it in Berlin on 20 January 1842. Although it was the fifth and final of Mendelssohn's symphonies to be completed, it was the third to be published, and has subsequently been known as Symphony No. 3.