From the best of my calculations, Conor is somewhere between 13 and 16 years old when he is wrongly accused of murdering King Nicholas. We know Conor is born above Paris in 1878. We know that in 1888, he is 10 years old. we know that in 1890, he is 12 years old.
We know that it is in the 1890s that he and his parents go to live on the Saltee Islands near Ireland. There he rescues Isabella from a fire and is rewarded by King Nichols; is taught by tutor Vigney; learns about flying; and witnesses from the castle keep Bolvilain's assassination of Nicholas and Vigney. In 1998, Conor would reach the age of 20, so it is reasonable to think that he was between 13 (1891) and approximately 16 when he was accused and imprisoned.
Connor was born in 1878. In the early 90s of that same century, he and his family move to the Saltee Islands where Connor befriends saves and Isabel. To his surprise, Isabel is the daughter of the king. The King, as thanks to Connor, agrees to let him study under the royal tutor. To clarify your question, both the King and Connor's tutor are murder. Connor witnessed these voracious murders at the meager age of 14. He is wrongly accused of murdering the King and is thus sent to prison.