With the signing of the Dayton/Paris Peace Agreement in 1995 the inter-Entity boundary lines were established along the former lines of confrontation. Four years of war destroyed many transport routes including the airports, roads, bridges, and railway lines, particularly along the inter-Entity boundary line. The international community identified the reconstruction of transport infrastructure as an essential priority. Transport routes were so badly damaged that many people who fled their homes to safer regions and other countries were unable to return even when they wanted to. The rehabilitation of transportation infrastructure between the two Entities of Bosnia and Herzegovina and the rest of Europe is therefore of great importance for the return of refugees and displaced persons, for the re-launching of economic activities, and to encourage freedom of movement and inter-Entity communications.

The EC has allocated over 80 MEURO to the rehabilitation of the transport sector.

In 1996 over 25 MEURO was allocated to the rehabilitation of the sector. The Essential Aid Programme (EAP) committed almost 17 MEURO to provide emergency equipment and supplies for transport rehabilitation in Bosnia and Herzegovina. A main project funded from the EAP budget was a 3 MEURO programme of rehabilitation for 23 km of road along the north corridor of Republika Srpska. Also in 1996 a 6 MEURO rehabilitation project was carried out on the Bosanski Samac Bridge which links the Republika Srpska and Croatia as well as a 2.8 MEURO project to rehabilitate the Sarajevo – Mostar – Caplina railway line. In addition, the 1996 "Europe for Sarajevo" programme initiated reconstruction work on Sarajevo Airport Terminal with an allocation of 3 MEURO.

The 1997 EC transport programme aimed to further increase trade and the movement of people, make all regions more accessible, and provide links to European transport networks. The programme allocated over 38 MEURO and focused on areas that would facilitate refugee returns. The programme was divided into four areas of reconstruction: airports including civil aviation, railways, bridges, and roads. A total of 4.5 MEURO was allocated to the rehabilitation of Mostar and Banja Luka airports, including repairs to buildings, hangars and control towers, supplies of electrical equipment, and navigation and communication systems. 3.7 MEURO was allocated to the rehabilitation of the Sarajevo airport. Over 10 MEURO was committed to reconstruction work on key rail and road bridges in the Republika Srpska, either linking the Entity to the Federation or to Croatia. An additional allocation of 4.8 MEURO was also provided for the reconstruction of the Samac Bridge at the Reconstruction involved the demolition of existing bridges, mine clearance where necessary, reconstruction and the provision of either railway lines or new roads. A total of 8.2 MEURO was allocated to the rehabilitation of the Sarajevo - Zenica - Novi Grad railway line at the Croatian border. Work encompasses Sarajevo to Zenica in the Federation, Doboj in northern RS, Banja Luka in western RS and Novi Grad. Assistance includes equipment and supplies, electrification, signaling and communications systems. Road rehabilitation amounted to a total of 5.45 MEURO. 2 MEURO of this was for the reconstruction and resurfacing of 91 km of badly damaged road from Kljuc in the western part of the Federation to Bihac near the Croatian border. Due to the EU’s regional approach on implementation of donated funds, the political situation in the hard-line Pale region of Republika Srpska in 1997 meant that conditionality had to be imposed on two road rehabilitation projects formally designated for that area. Instead, 2.7 MEURO was re-assigned to the rehabilitation of the Prijedor - Banja Luka - Derventa road in northern Republika Srpska.

In 1998 the EC allocated over 16 MEURO for further reconstruction work. 12.4 MEURO of this is for the continued construction of the work implemented in 1997 on bridges. The bridges are significant because they link Bosnia and Herzegovina to its neighbouring countries and join the two Entities. The Raca Bridge over the Sava River, for example, has received an allocation of 4.4 MEURO and connects the road and railway from eastern Republika Srpska to the Federal Republic of Yugoslavia. In addition, 1 MEURO has been allocated for support to the Civil Aviation Authority and a further 2.6 MEURO for the completion of the Sarajevo International Airport terminal.