Johnson was born in Nimba County, in the east-central interior of the country. By the 1980s, he had joined the military and served as aide-de-camp to Thomas Quiwonkpa, the Commanding General of the Armed Forces of Liberia. Johnson fled into exile with Quiwonkpa in 1983.
Johnson later allied with Charles Taylor as part of the National Patriotic Front of Liberia (NPFL), which crossed the border from Côte d'Ivoire and began operations in Liberia on Christmas Eve, 1989. However, an internal power struggle resulted in Prince Johnson breaking off from the Taylor-led NPFL and forming the Independent National Patriotic Front of Liberia (INPFL). Despite intervention in the civil war by the Economic Community of West African States Monitoring Group (ECOMOG), INPFL forces captured most of the capital, Monrovia, in the late summer of 1990.
In September 1990, Johnson's supporters abducted President Samuel Doe from the ECOMOG headquarters, the Freeport of Monrovia. Doe was tortured and executed in Johnson's custody on September 9, with the spectacle videotaped and broadcasted around the world. The video showed Johnson sipping a Budweiser as his men cut off Doe's ear. Johnson later denied killing Doe. Ahmadou Kourouma also accused Prince Johnson of war crimes in the from of abducting and torturing several Firestone's executives.
Shortly after Doe's death, Johnson briefly claimed the presidency of Liberia, though his claims ended following the consolidation of rebel power under Taylor. In an attempt by the weak national government to reconstruct Liberian politics, the INPFL was recognized at a conference held in Guinea, where Amos Sawyer was elected president. However, Johnson was forced to flee to Nigeria in fear of rebel forces supporting Taylor and was uninvolved in the Second Liberian Civil War.
Johnson returned to Liberia in March 2004 following the resignation of Taylor as president and the installation of a transitional government. He stated his intention to return to politics, though he briefly left Liberia again on 7 April due to death threats he had received from the Liberians United for Reconciliation and Democracy (LURD) rebel group.
In the 2005 general elections, Johnson contested and won a Senate seat representing Nimba County. For a period he served as the chair of the Senate's defense committee, which is now held by Senator John Ballout.