[9] The idea of a national land purchasing fund was first presented at the First Zionist Congress in 1897 by Hermann Schapira, a Lithuanian-Jewish professor of mathematics.

[15] The first parcel of land, 200 dunams (0.20 km2) east of Hadera, was received as a gift from the Russian Zionist leader Isaac Leib Goldberg of Vilnius, in 1903.

Over the years questions about the legitimacy of these transactions have been raised but Israeli legislation has generally supported the JNF's land claims.

After concentrating on the centre and northern part of the young state, the JNF-KKL started supporting Jewish settlements around the Negev border from around 1965.

By 1935, JNF had planted 1.7 million trees over a total area of 1,750 acres (7.08 km²) and drained swamps, like those in the Hula Valley.

[14] Over fifty years, the JNF planted over 260 million trees largely in semi-arid, rocky, hilly terrain in which cultivation is not cost-effective and the risk of land degradation is high.

[29] In 2006, the JNF signed a 49-year lease agreement with the State of Israel which gives it control over 30,000 hectares (300 km2) of Negev land for the development of forests.

The Israeli newspaper Maariv wrote that workers remove saplings daily to allow more tourists to plant the following day, but the JNF denied this and said it would sue the paper for libel.

[31] The Union for Environmental Defense has criticized the fund's forestry practices for "overreliance on highly flammable pine trees" and overuse of toxic herbicides, in the context of minimal government and public scrutiny.

In the 1980s, the JNF launched a project known collectively as "Operation Promised Land", to meet the challenge of the massive upsurge of Jewish immigration from the Soviet Union and Ethiopia.

[41] The plan has come under scrutiny as groups such as Bustan, Save the Negev, and Ohalah have expressed concern over the project's lack of transparency in light of the potential strain on ecological resources and the possible impacts on Bedouin communities nearby.

Documents by the JNF indicated that funds from the Canadian branch were used to fund projects including Camp Ariel Sharon in the Negev, an auditorium and training facilities at an Israeli Navy base in Bat Galim, and mess halls for the 124 Squadron and 131 Squadron of the Israeli Air Force at the Palmachim and Nevatim Airbases.

A 2014 document by the JNF notes that funds from its Canadian branch were used for a dozen "KKL for IDF" projects in the previous decade.

[46] A document by JNF's Canadian branch stated that it had helped develop an outdoor fitness area at a military base in Sde Boker for the Gadna program, which prepares young Israelis for IDF service.

Similarly, in 2014, the JNF Canada's Edmonton branch stated that it was funding a family visitation area, a plaza by the barracks, and an intake and release facility at Tze'elim Army Base.

[46] JNF's Canadian branch also helped construct a hilltop settler outpost, Givat Oz VeGaon, which was deemed illegal by the Israeli government and received at least 18 demolition orders from the Ministry of Defense.

[33] The tax-exempt status of the JNF-USA was challenged in 2011 as violating the public policy of the United States with respect to ethnic and religious discrimination.

JNF-UK launched a legal action to stop KKL using the names "JNF" or "Jewish National Fund" in the UK.

District Judge Geddes noted on KKL's "lack of independence from JNF UK"[53] The charitable status of the JNF-UK has come under increasing attack.

[60] In December 2021, JNF-UK Chairman Samuel Hayek was embroiled in controversy, following remarks that implied that Muslim immigration was endangering the future of British Jews.

[64] The CRA revealed 358 pages of documents explaining its decision, which outlined "repeated and serious non-compliance" with the laws governing charities.

[68] A bank clerk named Haim Kleinman in Nadvorna, Galicia placed a blue box labeled "Keren Le'umit" in his office and urged others to do the same.

[69] T'ruah has expressed concerns that the JNF is not transparent about where their funds go and that the organization may be subsidizing projects in West Bank settlements.

[71] A review of their tax filing from 2014 led Rabbi Jill Jacobs of T'ruah to estimate that about $600,000 of the $27.2 million in grants by JNF-USA went to support settlements.

[75] Israeli lawmakers have sought, unsuccessfully, to allow the State Comptroller to examine the books of the organization to determine whether the group's funds were being spent appropriately.

[78] Shortly afterwards, the Association for Civil Rights in Israel and the Arab Center for Alternative Planning also filed a petition to the Supreme Court challenging the ILA policy as discriminatory.

As a result of the Mazuz ruling, authorities found themselves facing a conundrum: on the one hand the JNF, as a "private" organization, had received donations from outside Israel which were specifically earmarked for the benefit of Jews; on the other hand, the state and the ILA (an agency of the state), which administered the land owned by the JNF, were banned from discriminating against non-Jews.

"[83] In September 2007, the High Court heard a further Adalah petition seeking cancellation of an ILA policy as well as Article 27 of the Regulations of the Obligations of Tenders, which in concert prevent Arab citizens from participating in bids for JNF-controlled land.

[87] In December 2011, Seth Morrison resigned from the board of JNF-USA in protest at the decision by Himnuta, a subsidiary of JNF-KKL, to launch eviction proceedings against the Sumarin family, who lived in the Silwan neighborhood of East Jerusalem.

[89] A campaign against the JNF's eviction was launched by Rabbis for Human Rights, the Sheikh Jarrah Solidarity Movement,[90] and the Jewish organization Yachad.