As agent for the Sierra Leone Company, Lieutenant Clarkson was instrumental in the founding of Freetown, today Sierra Leone's capital city, as a haven for chiefly formerly enslaved African-Americans first relocated to Nova Scotia by the British military authorities following the American Revolutionary War.

Because of his work in establishing Freetown, Clarkson is considered to be one of the founding fathers of Sierra Leone, alongside Granville Sharp, Thomas Peters, and Henry Thornton.

He was born in the Headmaster's house and, despite the early death of his father, continued to attend the school until 1777 when, aged 12, he entered the Royal Navy as a "young gentleman" on Captain Joshua Rowley's ship HMS Monarch.

Initially unmoved by what he had witnessed he later, likely influenced by his brother Thomas' passionate views concerning the immorality of slavery, came to abhor the institution and rendered practical assistance to the cause of abolition.

His brother Thomas, along with William Wilberforce and other members of the Committee for Effecting the Abolition of the Slave Trade, had incorporated the Sierra Leone Company with a view to resettling certain free and formerly enslaved blacks on the west coast of Africa.

Lieutenant Clarkson's charge was to secure among black communities of Nova Scotia, Canada, volunteers to settle in the area of the mouth of the Sierra Leone River.

Despite promises from the military, the settlements were underfunded, and authorities tended to favor white Loyalists, especially those from the South who had brought slaves with them to Nova Scotia, complicating the social situation.

From his work with the settlers in Nova Scotia and Sierra Leone, he grew to have great respect for them and struggled to ensure the company representatives did not take advantage of them.