Bahay Tuluyan was founded in 1987 in response to the growing number of street children in the Malate area of Manila. Bahay Tuluyan began as a drop in center, where children could go to have a bath, rest, eat or play. Many of the children visiting the center had nowhere to sleep, so the center quickly developed into a temporary shelter.

Looking for new and effective ways to reach out to children on the street, Bahay Tuluyan developed its alternative education program, using a 'Child-to-Child Approach'. The Child-to-Child Approach taps the enormous possibilities of participative learning and cooperative work for children.

Over the next decade Bahay Tuluyan developed various alternative education programs and expanded it's residential and emergency shelter program to include a satellite center for children in Quezon province which was first opened in 1999.

In 2003 Bahay Tuluyan entered into a partnership with Kibo Children’s House to take over the management of its center in Victoria, Laguna. Bahay Tuluyan began operating this center as a residential shelter for children, organic farm, research and training center.  The center has gradually been developed since then under a special project entitled 'Realizing the Dream'. 

In 2005 Bahay Tuluyan center for children in San Antonio, Quezon was completed and officially opened. The center included 3 family style homes, 2 group homes, recreation room, dining room, training center and organic farm.

Youth participation and advocacy progressed to a new level at Bahay Tuluyan in 2006 with the formation of 'PILAK' or 'Pinag Isang Lakas ng Kabataan', (United Strength of Youth), a youth advocacy group working to address issues affecting children.

In 2008 Bahay Tuluyan spearheaded the first Street Children’s Festival, held in Manila. The festival alongside the book ‘Sagip or Huli?: Rescue of Street Children in Caloocan, Manila, Pasay and Quezon Cities’ which was launched in 2009 boosted advocacy for children’s rights in the Philippines.

A highlight for Bahay Tuluyan in 2010 was the commencement of the 'Seeds of Change' project which, through community organizing, establishes grassroots child protection mechanisms in local communities.