The biggest recorded version of the song was by the Ted Weems Orchestra, with Elmo Tanner whistling. The recording was made in 1933 on Bluebird B-5131 to low record sales. Weems dissolved his band in early 1942 after leaving to fight in World War II. In early 1947, Kurt Webster, a disc jockey on WBT in Charlotte, North Carolina, a 50,000-watt station that reached across the East Coast, played Weems' version of "Heartaches". Webster enjoyed the tune and it entered his regular rotation, leading to listeners frequently requesting it and "Heartaches" gaining national attention and Weems reviving his band briefly to capitalize on the record's success. The 1933 recording was jointly released by RCA Victor Records as catalog number 20-2175 and Weems' 1938 re-recording on Decca Records as catalog number 25017. The Victor version first reached the Billboard magazine Best Seller chart on February 21, 1947 and lasted 16 weeks on the chart, peaking at number 1.
The recording by Harry James was released by Columbia Records as catalog number 37305. It first reached the Billboard magazine Best Seller chart on April 18, 1947 and lasted 3 weeks on the chart, peaking at number 8. This was his last charting hit.
A radically altered arrangement of "Heartaches" also became popular in 1961 as a version by The Marcels was released as a followup to their US hit "Blue Moon". Although the Marcels' "Heartaches" single failed to match the number 1 position on the US singles charts achieved by "Blue Moon", "Heartaches" reached the Top 10, peaking at number 7, as well as number 19 on the Hot R&B Sides chart. In addition to a vocal hook similar to that of "Blue Moon", the Marcels added to the introduction of the recording of "Heartaches" the group saying, then singing, "Watch out! Here we go again..."eventually this version sold over one million copies worldwide. The Marcels version is sampled in the 2016 Lonely Island song I'm So Humble featuring Adam Levine featured in the movie.
In 1963, Allan Sherman produced a parody version titled "Headaches," a commentary on television aspirincommercials. In the middle of the whistled part, a kid named Tom Greenleigh shrieks, "Mommy, can't you keep Daddy's car out of the driveway?!" At the end of the song, Sherman solved his headache problems by eating his television set.