Can I call a function with an if statement?

@OP; No, you can't. (Also, you're missing end statements.)

Scripts have a thing called "scope". Scope is every variable that the line being run has access to. local is used, for example, to declare scope within a code block:

local x = 5

if x == 5 then
	print(x) --> 5
	local y = "7"
	print(y) --> 7
end

print(x) --> 5
print(y) --> 7

--Because 'y' was declared locally, *within* the `if` block, it is removed from the scope when the `if` block ends.

Going a step higher, each individual Script has its own Scope. This includes LocalScripts.

The normal way to get around this is to use a global Table: _G or shared, however each Client (including the Server) gets its own copy of this Table. They are not replicated.

The only way to cross the Server<->Client boundary is through the Value objects (which don't work with FilteringEnabled) and the Remote* objects.

If you want a yielding function call, use a RemoteFunction (Yielding means that the LocalScript will wait for the invoked function to return before resuming.):

--Server script code
--(I have made this slightly more efficient, compared to your code.)
local A = Instance.new("Animation", char)
A.AnimationID = "ID here"

local RemoteFunc = Instance.new("RemoteFunction")
RemoteFunc.Name = "RemoteFunction"
RemoteFunc.Parent = game.ReplicatedStorage

function RemoteFunc.OnServerInvoke(player)
	Track = player.Character.Humanoid:LoadAnimation(A)
	wait(1)
	Track:Play() --Capitalization matters! In Lua, track ~= Track!
end
--THIS SHOULD ONLY RUN ONCE: do not put it inside of a PlayerAdded function.

--local script code
local RemoteFunc = game.ReplicatedStorage:WaitForChild("RemoteFunction")

game.Players.LocalPlayer.Character.Humanoid.Jumping:connect(function()
	RemoteFunc:InvokeServer() --You have to connect this event so that it runs every time. Unless you had other code that ran this repeatedly.
end)

If you want a fire-and-forget function call, use a RemoteEvent:

--Server script code
local A = Instance.new("Animation", char)
A.AnimationID = "ID here"

local RemoteEv = Instance.new("RemoteEvent")
RemoteEvName = "RemoteEvent"
RemoteEv.Parent = game.ReplicatedStorage

RemoteEv.OnServerEvent:connect(function(player)
	Track = player.Character.Humanoid:LoadAnimation(A)
	wait(1)
	Track:Play() --Capitalization matters! In Lua, track ~= Track!
end)
--THIS SHOULD ONLY RUN ONCE: do not put it inside of a PlayerAdded function.

--local script code
local RemoteEv = game.ReplicatedStorage:WaitForChild("RemoteEvent")

game.Players.LocalPlayer.Character.Humanoid.Jumping:connect(function()
	RemoteEv:FireServer()
end)