He is known for his extended expedition through the Uele River basin and onward towards the Nile, which was responsible for the deaths of over 1,800 people and established a Belgian presence in the region.

[3] Due to his energy and capability Van Kerckhoven was assigned various missions including purchase of land in Bas-Congo, recruitment of krooboys in Liberia and a 3-month exploration of the territory to the right of the Congo between Manyanga and Brazzaville.

On 3 August 1884 he was visited there by Lieutenant Van Kerckhoven who had been relieved of his command at Isangila and was concluding treaties with the tribes around Mukumbi.

[4] Van Kerckhoven passed through Léopoldville in April 1885, and was sent to succeed Camille Coquilhat in command of the Bangalas station, which he reached on 7 August 1885.

With the help of Ernest Baert and Francis Dhanis he began a large expansion in the region of rice, coffee and cocoa cultivation, built the first brick buildings and created new government posts.

[2] Jules Alexandre Milz arrived in Boma on 25 July 1888 and was assigned to the Bangalas District, where Van Kerckhoven was preparing for the Léon Roget expedition to the north.

[7] Always on the move on the small steamer Association Internationale Africaine, Van Kerckhoven was the first European to ascend the Itimbiri River.

[2] Van Kerckhoven came to the aid of the rearguard of the Emin Pasha Relief Expedition under Major Edmund Musgrave Barttelot, in Yambuya on the Aruwimi, and gave it supplies so it could continue its journey.

In his report to the governor general Van Kerckhoven recommended temporizing with the Arabs, but making every effort to prevent them from conquering territory upstream from the Bangalas, including a fortified camp at the mouth of the Aruwimi.

[2] At the time of Van Kerckhoven's Congo-Nile expedition, Arab slavers had occupied the Falls and were advancing northwest from there towards Djabir on the Uele River.

King Léopold II had ordered Captain Roget to establish an entrenched fortification in Basoko, at the mouth of the Aruwimi, and from there to extend a line of protective post north.

Léopold II now decided to send a strong expedition from the new bases to the Nile, blocking the north route to the Arabs and opening up a region that was still largely unexplored by Europeans since Wilhelm Junker's visit in 1871.

[2] Van Kerckhoven reached Boma on 2 December 1890 and led the main body of troops to the concentration point at the Bumba River, a little downstream from the Itimbiri.

Milz's term was over, but agreed to accompany Van Kerckhoven back to the Uele as second in command of his expedition to the Nile.

Van Kerckhoven made a short visit to the Falls to try to allay the fears of the Arab Rachid, then took the bulk of his men to Djabir.

At Ibembo he sent Milz to the Mbomou River to make every effort to gain the allegiance of Sultan Semio, who had been dealing with the Arab bands.

[7] The land force went through swampy country, covered with grassy hills along the ridge that separates the Uele and Bomokandi basins.

The local people were not hostile, and when the Barambo chief found the expedition was not an Arab band he entered into an alliance and let Captain Daenen establish a station.

[2] The column led by Van Kerckhoven and Milz reached the location of Amadi on 22 December 1891 where they started to build a post.

Milz, Gustave Gustin, Clément-François Vande Vliet and Semio, who had traveled by land along the south bank of the Uele, were attacked by the Barambo [fr].

They continued, making contact with the local chiefs and selecting sites for new posts, and reached the confluence of the Gada River with the Uele on 18 March, where they chose to build a new station at the village of Mbegu, named Niangara.

Although the Nzoro was 50–75 metres (164–246 ft) wide, only short sections were navigable, interrupted by falls and rapids that often extended for several kilometres.

[2] On 11 July Van Kerckhoven and Milz left by land along the south bank of the Nzoro through difficult country, with the soldiers carrying their loads for lack of porters.

"[11] In 1887 Van Kerckhoven told a fellow passenger on a steamboat, Roger Casement, that he paid his African soldiers a small fee for every rebel head they brought him after a battle, "to stimulate their prowess in the face of the enemy."

However, the historian Albert Chapaux considered that Van Kerckhoven was among the leading figures in the "development" of the Congo Free State.