KLM, the flag carrier of the Netherlands, abandoned the two countries at the height of their civil wars in the 1990s.
The new arrangement provides three schedules per week - Wednesdays, Fridays and Sundays, direct from Amsterdam and returning via Monrovia.
Sierra Leone says return of airline demonstrates confidence of international community in the country and its economy.
The Dutch airline, KLM, has announced the resumption of flights to Freetown in Sierra Leone and Monrovia in Liberia for the first time in 20 years.
The flag carrier of the Netherlands, which owns slightly more than a quarter of Kenya Airways (KQ), abandoned the two countries at the height of their civil wars in the 1990s.
In Sierra Leone, the last KLM flight left on December 25, 1996.
KQ also resumed its flights to Liberia and Sierra Leone in September 2015 after Kenya's Health ministry lifted a ban placed the year before restricting travel following outbreak of the Ebola virus.
Three schedules
The new KLM arrangement provides three schedules per week - Wednesdays, Fridays and Sundays, direct from Amsterdam and returning via Monrovia.
Sierra Leonean Transport and Aviation minister Leonard Balogun Koroma, received the maiden flight on Sunday night at the Freetown International Airport, with 110 passengers on board.
He said the return of KLM demonstrated the confidence the international community had for the country and its economy, adding that the addition would induce competition, thereby ensuring better service and prices for customers.
KLM brings to seven the number of international flights now operating in Sierra Leone, after most of the nine airlines operating in the country prior to the Ebola epidemic ceased operations.
The airline said in a statement that the inauguration of the Amsterdam route would reduce flying times each way and give great connection opportunities to destinations worldwide via its hub of Amsterdam Schiphol.
The Sierra Leonean aviation industry was still recovering from the effect of the 2014 Ebola epidemic, which forced the termination of operations by all the airlines at the time, except for Royal Air Maroc and Brussels Airlines.
The scarcity of airlines left Sierra Leone as one of the most expensive places to fly to and from.
KLM becomes the third major European airline to fly to Sierra Leone, after Air France and Brussels Airlines.
The Sierra Leone Airport Authority (SLAA) said negotiations to have KLM return lasted six months.
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