I'm designing a character for a campaign whose role is to be a recurring antagonist. When the players first meet him, I want him to seem undeniably human. The idea is that the party will "kill" him and his body will be destroyed, only for him to be revived later and come back for revenge as Lich.

The party will be able to check him for magical effects when they first meet and I want it to be a surprise that he is a Lich. If they party detects Transmutation or Illusion magic on him or detect him as Undead it will give too much of a hint to his true nature.

Is there a way the Lich could retain a human form without magic?

He's still alive when the PCs meet him, but his phylactery is ready to go

Although it's widely believed that a lich must always commit suicide as part of the process of attaining lichdom, that's D&D canon, not Pathfinder. In fact, in Pathfinder, the process of lichdom is unique to the individual (wiki/SRD):

The spellcaster must first research the construction of a phylactery, and then discover the means by which to transfer their soul into the receptacle. As no two bodies or souls are the same, each of these processes are unique to the individual; what has worked in the past might kill or drive another person insane.

It's plausible that you might meet a spellcaster who has completed their phylactery, but has not yet died once. He's currently enjoying his remaining time as a living being, which has its advantages (moving openly in human society, enjoying pleasures like food and drink, raising a family and so on). When the PCs kill him, the phylactery works as intended and he is raised as a lich, and now he's really mad at the PCs for spoiling his plans.

Here are some things that may help the lich from being ousted for his trickery. Some can even allow him to use magic.

Skills

• 
  Disguise: Magical means of detection do not foil mundane disguise checks, with a high enough check the players will be unable to tell.

Feats

• 
  Civilized Ghoulishness: As a GM you may consider allowing this feat to work on the Lich, granting a +10 bonus to disguise checks.

Spells

• 
  Greater magic Aura: Greater magic aura would allow the Lich to hide any magical auras they have (from spells or items that may be on them) or only show a specific fake aura.


• 
  Nondetection: Nondetection prevents any "detect x" spells from working against the subject of the spell, preventing the detection of their spell auras, unless they succeed at a CL check.


• 
  Mask Against Divination: Works similarly to nondetection, excepts it stops more spells and helps against skill checks to find out information against them.


• 
  Mind Blank: Mind blank stops all divination spell from working against the subject.


• 
  Daywalker: This physically reshapes an undeads body to resemble a living creatures, creatures that interact with it get a perception check to notice it's disguise.


• 
  Fleshy Facade: This spell makes the creature look like it did when it was alive. Doesn't work on skeletons and fleshless undead, so depending on how you interpret a lich to look like, it may or may not work.

Magic Items

• 
  Iron Circlet of Guarded Souls: This protects the wearer from any spells that Nondetection stops, except there is no caster level check to overcome it.


• 
  Shawl of Shadowy Disguise: This item puts you under a constant conjuration spell (unusual for a disguise spell), that only lets people who see you determine vaguely determine things about you, such as being humanoid in shape, swinging some sort of weapon. This keeps players from determining any information about the enemy.


• 
  Necklace of Fireballs: Since you're destroying the body might as well go out in a burst of flame. Combine fireball with Deadman's contingency to detonate it.


• 
  Hood of Privacy: This item allows you to thwart a divination attempt against you, either blocking it, or giving it a false reading.

Use undetectable magic

For example, the spell Nondetection prevents divination magic from detecting you. Spells like Detect Magic and Detect Evil and Good are divination magic.

The Disguise skill is what you are looking for.

Note though that a standard kit may not have enough material in it but the lich can make up their own kit that has enough putty to make a face, etc.

It wouldn't be great but it may work if the lich or one if its lackeys has a high enough skill.

From the table below, I would take at least Different gender, race, and age.

Table: Disguise DCs and Modifiers 
Disguise Disguise Check Modifier 
Minor details only +5
Disguised as different gender1 –2 
Disguised as different race1 –2 
Disguised as different age category1 –2 
Disguised as different size category1 -10

Though, as a GM, I'm likely to give it a flat -10 for all the fake stuff you have to layer onto the face.

An obvious mask would lower the DC of the disguise but would be suspicious in and of itself.

Another possibility that just occurred to me:

A flesh golem. Use the rules for creating a golem as armor.

I'm not sure that, as a GM, I would let that one fly but it's worth a shot.

Check out Building and Modifying Constructs and go down to Construct Armor under Complex Modifications.