Phillip Weaver, 26, of Amethyst Road, in Hull, appeared at Hull and Holderness Magistrates' Court.
The 51-year-old woman was pushed off her bike before being subjected to a serious sex assault in the Woodhall Street area of the city, Humberside Police said.
Mr Weaver was ordered to appear at Hull Crown Court on 2 September.
A man has appeared in court charged with two counts of raping a cyclist in Hull during the early hours of Tuesday.