Shirley Thompson, the youngest of the Thompson sisters, joined the New Orleans Congress of Racial Equality (CORE) Freedom Rides as they tested the Interstate Commerce Commission’s desegregation of bus transit. At eighteen years old, and just a few days after graduating from George Washington Carver High School, Shirley boarded her first Freedom Ride on June 6, 1961, to Jackson, Mississippi. 
The previous Freedom Rides into Mississippi were met with violence, an increase in jail penalties from two months to four, and a request from President John F. Kennedy to the Freedom Riders for a “cooling-off period.” However, CORE leaders remained diligent in their protests and continued ahead with their Freedom Rides and sit-ins across Mississippi.  Because of CORE members’ vigor and determination to fight white supremacy, police jailed activists for their continued acts of civil disobedience, imprisoning Riders in the Parchman State Penitentiary when local jails exceeded capacity.
Police arrested Shirley Thompson for “breach of peace” while attempting a sit-in within a waiting room. Given the increased sentence of four months, police took Shirley to the Parchman State Penitentiary.  While there, Shirley stated that “she was slapped by police officers.”  CORE activist Abdul Aziz Khaalis documented the brutalities at Parchman State Penitentiary in his diary, later published online as a series entitled Letters to My Children. Khaalis stated:
"Yes, they took our mattresses from us. We still sang freedom songs. Yes, they took our clothes. Yes, we froze when our bodies touched the steel bunks with the air turned on high. Yes, we were eaten by insects released from jars into the cell block with the air turned off and the windows closed to make it hot like hell as we were bitten and eaten everywhere. Yes, they dragged a screaming white Freedom Rider past our cells. They had a wrist breaker attached to his right arm. It was a handcuff with big screws that hit the nerve points in his wrist. It was attached to a chain with a wooden handle. They dragged him, flipped the chain, making his body flip like a fish from the agony he experienced, and I felt it In my cell and still hear his screams when I have the memory. Yes, they put stuff in our food to give us the runs. Yes, they were devil-mean hateful jailers." 
While newspapers reported one piece of Shirley’s testimony from within the walls of Parchman State Penitentiary, Shirley likely faced other violence as well. Jean Thompson posted a bond for her sister and the prison released her. Shirley’s release date is unknown.
Before her death at age 47, Shirley also participated in the 1962 Louisiana Freedom Summer, 1962 Mississippi Freedom Summer, and 1963 March on Washington alongside her sister Alice Marie Thompson.