"Polling has ended with overwhelming response," Dasho Kunzang Wangdi, Bhutan's chief election commissioner, said in the capital Thimphu.
However, several complaints had been made by voters saying they were unable to vote because of bureaucratic glitches.
"Some people applied for their voter card quite late so they could not receive them on time," Wangdi said.
The tiny, conservative Himalayan kingdom has been preparing for polls since the former monarch decided to hand power to an elected government.
Members of the National Council are barred from joining political parties.
However, polls will take place in February and March to elect the 75-member National Assembly where newly formed political parties can take part.
Final turnout figures were not available but many of Bhutan’s over 300,000 eligible voters walked for hours from distant villages across the mountain slopes to cast their vote.
"I came along with my husband and two sons early in the morning. We are now part of history having cast our votes," Pema Dorji, a school teacher said.
But many Bhutanese view the looming changes with trepidation.
"To be frank we want the monarchy to continue. But with the king deciding to usher in democracy there is no option and so we are praying that this new system works well," said an elderly monk.
Many candidates were in their twenties, partly because the rules required all candidates to be university graduates.