Kroos' contract with the Bundesliga champions expires at the end of next season and has so far not agreed to a new deal.
A potential transfer away from the Allianz Arena has been mooted, with Premier League side Manchester United - who face Bayern in the UEFA Champions League quarter-finals first leg on Tuesday - linked with the midfielder.
The 24-year-old has previously hinted that he would be keen to play in England, but Rummenigge has moved to end the speculation over Kroos' future.
"Toni Kroos is sure to play in a Bayern Munich shirt next year as well," Rummenigge said ahead of Bayern's clash at Old Trafford.
Kroos has established himself as a regular with Bayern and was a key part of the side that won the Bundesliga, Champions League and DFB-Pokal last season.
The Germany international has made 41 appearances in all competitions for Bayern this term, scoring three goals.
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