Michael Leaberry, of Saltney, eluded police for almost 18 months after his initial arrest for the offence in September 2015.
He was jailed for 12 years at Mold Crown Court on Thursday after admitting rape, sexual assault and incitement.
The child's mother said Leaberry had left a "trail of devastation".
Leaberry - also known as Stephen Bugman - failed to turn up for further questioning after being bailed by police in 2015.
He was eventually arrested in Bournemouth in February after a tip-off from a member of the public following a Crimewatch appeal.
He had been living under a false name and claimed to be a victim of modern slavery.
Mark Connor, defending, said Leaberry had "deepest sorrow" for what he had done and had been abused as a child himself.
Judge Rhys Rowlands said: "How anyone could view a child this young as a sexual object is quite shocking."
A Flintshire man who went on the run after raping a young child has been jailed for 12 years.