Colorado State University's enrollment doubled during the 1960s, making it the city's primary economic force by the end of the century. By 2017, the university was employing 7,829 people--nearly double the work force of the next largest employer.

In July 1997, the city experienced a flash flood after 10-14 inches (250-360 mm) of rain fell during a 31-hour period. The rainfall was the heaviest on record for an urban area of Colorado. Five people were killed and $5 million in damages were dealt to the city. The waters also flooded Colorado State University's library and caused about $140 million in damages to the institution.

William Avery--brother to Franklin Avery, who founded First National Bank and built the Avery House--died in Fort Collins in 1890 of an assumed stomach ailment. When his wife, Mary, married her late husband's business partner, Frank Millington, 12 days later, people began to suspect foul play. Although Avery's body was exhumed and death by arsenic poisoning was whispered around town, Mary and Millington were eventually acquitted. Today, the Avery House is considered a National Historic Landmark and visitors can wander its 17th century rooms and hallways. But some visitors claim to have witnessed strange activity inside these historic walls, including reports of an unhappy spirit in the middle upstairs bedroom.