The 27-year-old - currently sidelined with a thigh injury - has been with the club since 2001 and was due to see his deal expire in 2017.
However, in his 15th season with Schalke, the Germany international put pen to paper on a contract extension that keeps him tied down until June 2020.
"My heart was thumping when I put pen to paper," Howedes told the club's official website.
"Schalke 04 is a great club with amazing fans, a club I am thankful to for developing me as a youth player in the Knappenschmiede academy, giving me the opportunity to make my breakthrough in the Bundesliga as a youngster and handing me the role of captain early on.
"We have a young team full of potential and ambition. I want to continue shaping its future."
The Germany international has made 206 Bundesliga appearances for Schalke, scoring 11 times, as well as making 23 DFB-Pokal outings and 55 more in European matches.
"We're delighted that Benedikt has taken this step, as it is a sign of real commitment to Schalke 04 from a leading player," added sporting director Horst Heldt.
"It shows that he has faith in our plans, in which he plays an important role as team captain and defensive stalwart."
Howedes made his Bundesliga debut in 2007 and, having won the DFB-Pokal in 2011, was made captain a year later before becoming the first player from the club to win the World Cup in 2014.