Opening batswoman Mandhana and leg-spinner Yadav were also included in the ICC Women's ODI Team of the Year, which has New Zealander Suzie Bates as captain.
The ODI and T20 sides were selected by a voting academy, which has former players like Lisa Sthalekar, Charlotte Edwards, Anjum Chopra and members of the media, and took into consideration performances in the 2018 calendar year.
Harmanpreet has been rewarded for spearheading India to the semifinals of the ICC Women's World T20 2018 in the West Indies in November.
"In that tournament, (Harmanpreet) Kaur scored 183 runs at a strike-rate of 160.5, while in the 25 matches in the calendar year, she accumulated 663 runs at a strike-rate of 126.2. Kaur is ranked third in the MRF Tyres ICC Women's Player Rankings for T20I Batters," the ICC said in a statement.
The 29-year-old Harmanpreet said she was surprised to have been named the captain of the World T20 XI.
"To be honest, it was really surprising for me. The last two years we did not get enough T20I matches to play and it was really tough for me to build that confidence in the team and show that self-belief that we can do well in T20Is. Credit goes to all team members, the way they worked hard and show that self-belief," Kaur said.
"This award means a lot to me to build my confidence, BCCI is showing confidence on me - that I can do well in the format and I am looking forward to doing well in the future."
The T20I team has players from five countries, including four from the ICC Women's World T20 2018 champions Australia. Two players are from New Zealand and one player each from Bangladesh and England, besides the three from India.
Rumana Ahmed is the first Bangladesh player to have been selected in the ICC squad. The right-arm leg-spinner has been the second most successful T20I bowler in the 2018 calendar year with 30 wickets in 24 matches, including four wickets in four matches in the ICC Women's World T20 2018.
The ODI team, on the other hand, has players from seven countries, with two each from England, India, New Zealand and South Africa. Australia, Pakistan and West Indies have one player each.
Bates' appointment as the ODI captain was a recognition of her contribution in inspiring her side to the second position in the ICC Women's Championship after three rounds.
In the seven ODIs this calendar year, Bates has scored 438 runs with two centuries and a half-century. Bates is presently ranked seventh in the MRF Tyres ICC Women's Players Rankings for ODI Batters.
Besides India's Mandhana and Yadav, Australia's Alyssa Healy and Suzie Bates of New Zealand are the other players who feature in both the ODI and T20I squads.
ICC Women's ODI Team of the Year (in batting order): Smriti Mandhana (India), Tammy Beaumont (England), Suzie Bates (New Zealand; captain), Dane van Niekerk (South Africa), Sophie Devine (New Zealand), Alyssa Healy (Australia; wk), Marizanne Kapp (South Africa), Deandra Dottin (West Indies), Sana Mir (Pakistan), Sophie Ecclestone (England), Poonam Yadav (India).
ICC Women's T20I Team of the Year (in batting order): Smriti Mandhana (India), Alyssa Healy (Australia; wk), Suzie Bates (New Zealand), Harmanpreet Kaur (India; captain), Natalie Sciver (England), Ellyse Perry (Australia), Ashleigh Gardner (Australia), Leigh Kasperek (New Zealand), Megan Schutt (Australia), Rumana Ahmed (Bangladesh), Poonam Yadav (India).