Yep! Just add
S.CFrame = S.CFrame * CFrame.Angles(math.rad(-180), 0, 0)
before the line with the code
S.Parent = game.Workspace
If the angle is still off, or isn’t the right axis, then mess around with the number or relocate the math.rad(-180) to a different axis. Hope this helps! 
Thank you! Ill let you know if anything happens!
No problem! Hope it helps!
Ok, so it shoots in the mouse direction which is good!
But it faces sideways still, here’s the code i’m using:
local S = script.ThrowingSpear:Clone()
S.CanCollide = false
S.Anchored = false
local y = Instance.new("BodyVelocity")
y.maxForce = Vector3.new(math.huge, math.huge, math.huge)
local SC = plr.Character.Torso.CFrame * CFrame.new(6, 0, 0)
S.CFrame = CFrame.lookAt(SC.Position, MousePos)
y.Velocity = S.CFrame.lookVector * 50
S.Parent = game.Workspace
S.CFrame = S.CFrame * CFrame.Angles(math.rad(-180), 0, 0)
y.Parent = S
S.PlayerName.Value = plr.Name
game.Debris:AddItem(S, 5)
It faces sideways when it fires, which isn’t wanted. Thank you!! : D
Hey! So sorry for late reply, but try math.rad(90) or math.rad(-90) instead of math.rad(-180). Sorry for the mistake. You didn’t specify how it was rotated so I assumed it was pointing towards the player instead of towards the mouse, apologies!