A Secret Bonus Point is awarded to our hero Headdy each times he discovers some kind of secret and each one increases your final score by a number. Their number varies with the stages, and there are 39 in the game in total. They are often related to hitting the curious [[
- Destroy the Robo-Collector before it leaves the screen.
- Complete Headcase's practice stage.
- Complete Hangman's practice stage.
- Complete Beau's practice stage.
- Knock the green soldier off the watch tower (BEFORE destroying it with the ball).
- Destroy Old McGee (first defeat Catherine Derigueur).
- Destroy Mule McGee (first defeat Catherine Derigueur).
- Defeat Snake Eyes (choose the path that requires the Spike Head instead of the one that requires Pin Head).
- Wait for Mad Dog will drop Bino, then strike him twice.
- Destory a smiley balls released by the second ball machine.
- Wait for Trouble Bruin to release a puppet with a blue head, then strike it.
Act 3 : There are four Secret Bonus Points in this act.
- In Down Under, wait for the second ball machine to start releasing smiley balls and destroy one of them.
- In Backstage Battle, wait for Trouble Bruin to release a puppet with an inflated head and destroy it.
- In The Green Room, destroy the Puppeteer before Gentleman Jim.
- In Clothes Encounters, wait for the Wooden Dresser to put on a Bino costume and destroy it.
Act 4 : There are seven Secret Bonus Points in this act.
- In Terminate Her Too, keep hitting one of the orbs at the beginning. Later, destroy one of the cannonballs shot by the Super Tank Machine, then destroy the frog statue blocking the water.
- In Mad Mechs, destroy all five blue blocks with the Hammer Head.
- In Mad Mechs 2, destroy the two fans. Just hit them everytime they turn back on until they are destroyed.
- In Heathernapped, wait for Bino to come down to clean the windows and destroy him.
Act 5 : There are three Secret Bonus Points in this act.
- In Stair Wars, wait before destroying Trouble Bruin and continue climbing the tower. At some point, you will get the Secret Bonus Point.
- In Towering Internal, don't take any damage before destroying the two arms and reaching the platform above. You also have to do it within a certain time limit.
- When fighting Spinderella, in the stage of the same name, at some point, Bino will start walking around the screen. Hit him until he is destroyed.
Act 6 : There are three Secret Bonus Points in this act.
- In The Flying Game, wait until the Headcase at the beginning shows a Bino head and hit it. A bit later, one of the rockets will have a dog in the window, destroy it.
- When fighting Baby Face, in the stage of the same name, keep shooting the Grandpa Face and don't let him grab you. Once you destroy it, you will see Bino tied to the pole, shoot him to free him.
Act 7 : There are 3 Secret Bonus Points in this act.
- In Headdy Wonderland, one of the cows will make a different noise when jumped on; Destroy it by hitting it in the back. Just before the fight with the Gatekeeper, there's a totem pole with a bird-like man sitting on it; Hit that, too. During the fight, the Gatekeeper might bring in Bino, hit him.
Act 8 : There are six Secret Bonus Points in this act.
- In The Rocket Tier, collect every bonus item on the screen.
- In Illegal Weapon 3, hit one of the falling Soldiers after destroying the Missile Man.
- In Fun Forgiven, hit Tarot's heart ball three times. After fighting him, there are three "Shoot Here" blocks at the top of the platforming section. Hit the one near the exit to get the point.
- In Vice Versa, stand next to Sparky and hit three fireballs.
- While fighting Twin Freaks, hit the Bino head that he launches.
Act 9: There are four Secret Bonus Points in this act.
- In Fatal Contraption, destroy every block. When you reach the platform with Cocoa on it, hit it to receive your Secret Bonus Point.
- In Far Trek, avoid Trouble Bruin for one minute.
- During the green orb attack in Finale Analysis, use the Hammer Head to destroy all of the spikes that fly up from the bottom.