The striker, who was born in Sudan but grew up in Australia from the age of nine, confirmed his departure and his new club via Twitter on Tuesday.
Mebrahtu joined the Czech side in 2016 from Western Sydney Wanderers.
"I would like to announce my time with Mlada Boleslav has come to an end through mutual agreement," he tweeted.
"Thank you to the staff, players and of course the fans for their support.. I wish you all the best! The past 2 years has been a journey of growth and filled with good memories.. but now it's time for a new challenge!!
"Looking forward to the future! A special mention to the PFA for their support in this process, specifically Angela Collins and Jon McKain!"
Mebrahtu had not featured in any of Mlada Boleslav's five games this season. The 27-year-old scored nine goals in 21 appearances last season and 10 in 26 the campaign before.
He signed a one-year contract extension with the Czech First League outfit in January.
Sparta Prague are the biggest club in the Czech Republic with 33 league titles won in their 124-year history.
Mebrahtu started his career with Gold Coast United and also spent two seasons with Melbourne Heart.