Yes but not many companies have them new anymore as it is harder and harder to find parts for such computers.

Interloper.com has a few configurations that are new computers with ISA slots. Here are a couple of examples:

Interloper SC16 System:

High End Intel Quad Core Computer with 2 ISA slots

 

• Mid Tower case with power supply
  

  High End Intel Quad Core Computer with 2 ISA slots

• Socket 1150 motherboard with:
  • 1 PCIe x16 Gen 3 slot (PCIe 3.0)
  • 1 PCIe x4 Gen 2 slot (PCIe 2.0) – x1 signal
  • 4 PCI slots (PCI 2.3)
  • 2 ISA slots
• Intel Quad Core i5-4590S 3.00GHz 6MB 5GT/s LGA 1150 CPU
• 8GB DDR3 memory – upgradeable to 16GB
• 500GB SATA hard drive
• DVD-R/RW drive

 

 

Interloper SC4 System:

 

• Mid Tower case with 400W power supply
  

  New Pentium 4 computer with 3 ISA slots

  
  

• Pentium4 Socket 478 motherboard with 3 ISA slots, 2 PCI and 1 AGP
• Intel Pentium 4, 2.8GHz CPU
• 1GB memory – upgradeable to 2GB
• 80GB hard drive
• Floppy drive
• DVD-R/RW drive
• Standard Audio
• Standard video
• 10/100 Ethernet LAN
• 2 x 9 pin serial ports

Interloper SC5 Rackmount System:

The SBC (single board computer) comes with:

• Pentium 4, 3.0 GHz CPU
  

  4U rackmount system with 9 ISA slots – New

• 1 GB DDR memory
• On-board video
• On-board 10/100 LAN
• Active PICMG Backplane with:
  • 9 ISA slots
  • 4 PCI slots
  • 1 PICMG slot for SBC

If you need a custom configuration, call them. They may have an alternate solution for you.