A trader borrows 5000 from a financial institution at 4% rate of interest per annum. He repays 1000 at the end of each year. How much does he still has to pay after the third year?

The trader borrowed 5000 at a 4% rate of interest per annum. Therefore, the interest on the loan per year is 5000 * 4/100 = $<<5000*4/100=200>>200.

He repays 1000 at the end of each year, so after the first year, he still has to pay 5000 + 200 - 1000 = $<<5000+200-1000=4200>>4200.
After the second year, he still has to pay 4200 + 200 - 1000 = $<<4200+200-1000=3400>>3400.
After the third year, he still has to pay 3400 + 200 - 1000 = $<<3400+200-1000=2600>>2600. Answer: \boxed{2600}.