Limiting ourselves to the twentieth century, we find 3 women that led wars:

Indira Priyadarshini Gandhi:
(19 November 1917 – 31 October 1984) She was an Indian politician, she was the 3rd prime minister of India and was also the first and, to date, only female prime minister of India.

She served as prime minister from January 1966 to March 1977 and again from January 1980 until her assassination in October 1984, making her the second longest-serving Indian prime minister.
She went to war with Pakistan in support of the independence movement and war of independence in East Pakistan, which resulted in an Indian victory and the creation of Bangladesh, as well as increasing India's influence to the point where it became the sole regional power of South Asia.
In 1984, after Gandhi ordered military action in the Golden Temple of Amistrar in Operation Blue Star, her military action claimed the lives of hundreds of Sikhs.
On 31 October 1984, two of Gandhi's Sikh bodyguards shot her with their service weapons in the garden of the prime minister's residence allegedly in revenge for Operation Blue Star.

Margaret Thatcher:
She was Prime Minister of the United Kingdom from 1979 to 1990 and Leader of the Conservative Party from 1975 to 1990. The longest-serving British prime minister of the 20th century, she was the first woman to hold that office.

The conflict began on 2 April 1982, when Argentina invaded and occupied the Falkland Islands, followed by the invasion of South Georgia the next day. On 5 April 1982, the British government dispatched a naval task force to engage the Argentine Navy and Air Force before making an amphibious assault on the islands. The conflict lasted 74 days and ended with an Argentine surrender on 14 June 1982, returning the islands to British control. In total, 649 Argentine military personnel, 255 British military personnel died as a result of the war.


Sirimavo Bandaranaike:
Sirimavo Bandaranaike was elected the modern world's first female head of government in 1960 when she became prime minister of Sri Lanka, or Ceylon as it was known then. She entered politics after the assassination of her husband Solomon Bandaranaike in 1959.

When she became Prime Minister of Sri Lanka in 1960. She served three terms: 1960–1965, 1970–1977 and 1994–2000.
She is from a majority tribe in Sri Lanka called the Sinhalese. Her pro-Buddhist and pro-Sinhalese policies alienated the Tamil minority, continuous discrimination, her decision to drop English as an official language and her order to conduct all government business in Sinhala, the language of the majority Sinhalese, violent persecution against Sri Lankan Tamils by the Sinhalese dominated Sri Lankan Government.
Sirimavo Bandaranaike pursed policies that encouraged the Buddhist religion, promoted Sinhalese and Buddhist culture, which alienated the Tamil minority. Further problems arose with the President's state takeover of foreign businesses, particularly the petroleum companies, which upset the Americans and the British, who imposed an aid embargo on Sri Lanka. As a result, Bandaranaike moved her country closer to China and the Soviet Union and championed a policy of nonalignment or of neutrality in international affairs.

A civil disobedience campaign was instigated by a part of the country's minority Tamil population who were outraged by her actions which they considered a highly discriminatory act and an attempt to deny Tamils access to all official posts and the law. This led to an increase in Tamil militancy which escalated under succeeding administrations.
Her actions resulted in a bloody civil war. From July 1983-2009, about 80,000 - 100,000 people lost their lives in the 25 years civil war.

She earned her place in history as the world's first ever female prime minister and as mother of her nation's first female head of state.

She remained in office just a few months before her death, but had little real power. She died on election day, having cast her vote for the last time.

What of Patience Jonathan of Nigeria??