President Compaore faced 11 contenders, however the opposition failed to rally a single candidate.
Opposition candidate Herman Yameogo withdrew from the race last month in protest against President Compaore's candidacy.
The opposition said that President Compaore should not have been allowed to run for a third, consecutive term, according to new election laws limiting presidents to just one term in office.
However the High Court ruled that, because the new law had gone into effect in 2000, after President Compaore's last electoral victory, it did not apply to him.
Residents say 54-year-old President Compaore's firm grip on power since his 1987 coup has made his party a daunting political machine.
Nearly four million of the West African nation's 12 million people were registered to vote, with 12,000 polling centres across the dusty, impoverished nation, Electoral Commission Chairman Moussa Michel Tapsoba said.
People waited in long lines outside schools in the capital, some seeking shade under trees in the scorching sun.
President Compaore, long accused of helping fuel armed conflict across West Africa, won two previous elections for seven year terms.
The West African nation's first multiparty presidential election in 1991 was marked by widespread violence.
Subsequent votes have been held peacefully, including the 1998 presidential vote in which President Compaore won 87.5 per cent.
About 1,000 observers were monitoring the poll, including 600 foreigners.
Senator Laurent Beteille, one of the observers representing the international Francophonie Movement, said on national television after the vote ended that, in the three provinces where they were present "the voting was generally smooth."
Burkina Faso is among the world's poorest countries, with high rates of unemployment and illiteracy. The country was buffeted for decades by military coups after gaining independence from France in 1960.